CRAN Package Check Results for Package rbioacc

Last updated on 2025-07-23 21:51:56 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.2.1	397.61	200.88	598.49	ERROR
r-devel-linux-x86_64-debian-gcc	1.2.1	329.20	165.11	494.31	ERROR
r-devel-linux-x86_64-fedora-clang	1.2.1			896.19	ERROR
r-devel-linux-x86_64-fedora-gcc	1.2.1			1096.37	ERROR
r-devel-windows-x86_64	1.2.1	387.00	233.00	620.00	ERROR
r-patched-linux-x86_64	1.2.1	402.08	221.41	623.49	ERROR
r-release-linux-x86_64	1.2.1	393.66	221.22	614.88	ERROR
r-release-macos-arm64	1.2.1			254.00	OK
r-release-macos-x86_64	1.2.1			341.00	OK
r-release-windows-x86_64	1.2.1	392.00	235.00	627.00	ERROR
r-oldrel-macos-arm64	1.2.1			132.00	NOTE
r-oldrel-macos-x86_64	1.2.1			165.00	NOTE
r-oldrel-windows-x86_64	1.2.1	441.00	301.00	742.00	ERROR

Check Details

Version: 1.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [34s/39s] 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 5.4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.008 seconds (Sampling) Chain 1: 0.012 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 3.1e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: 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: 0.016 seconds (Warm-up) Chain 2: 0.007 seconds (Sampling) Chain 2: 0.023 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: Chain 1: Gradient evaluation took 0.000141 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.41 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: 0.013 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.014 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000113 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.13 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.001 seconds (Sampling) Chain 2: 0.008 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 6.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.65 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: 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 5.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.59 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 1). Chain 1: Chain 1: Gradient evaluation took 3.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.005 seconds (Sampling) Chain 1: 0.012 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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 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 0.000151 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.51 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: 0.007 seconds (Warm-up) Chain 1: 0.005 seconds (Sampling) Chain 1: 0.012 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 0.000111 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.11 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: 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 3.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 10 [ 10%] (Warmup) Chain 1: Iteration: 2 / 10 [ 20%] (Warmup) Chain 1: Iteration: 3 / 10 [ 30%] (Warmup) Chain 1: Iteration: 4 / 10 [ 40%] (Warmup) Chain 1: Iteration: 5 / 10 [ 50%] (Warmup) Chain 1: Iteration: 6 / 10 [ 60%] (Sampling) Chain 1: Iteration: 7 / 10 [ 70%] (Sampling) Chain 1: Iteration: 8 / 10 [ 80%] (Sampling) Chain 1: Iteration: 9 / 10 [ 90%] (Sampling) Chain 1: Iteration: 10 / 10 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.002 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 2.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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 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 0.000116 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.16 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: 0.004 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: Chain 2: Gradient evaluation took 0.000124 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.004 seconds (Sampling) Chain 2: 0.007 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 4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 3.2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds. Chain 2: Adjust your expectations accordingly! 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 3). Chain 3: Chain 3: Gradient evaluation took 3.1e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.31 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: 0.005 seconds (Warm-up) Chain 3: 0.003 seconds (Sampling) Chain 3: 0.008 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 2.3e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds. Chain 4: Adjust your expectations accordingly! Chain 4: Chain 4: Chain 4: WARNING: No variance estimation is Chain 4: performed for num_warmup < 20 Chain 4: Chain 4: Iteration: 1 / 10 [ 10%] (Warmup) Chain 4: Iteration: 2 / 10 [ 20%] (Warmup) Chain 4: Iteration: 3 / 10 [ 30%] (Warmup) Chain 4: Iteration: 4 / 10 [ 40%] (Warmup) Chain 4: Iteration: 5 / 10 [ 50%] (Warmup) Chain 4: Iteration: 6 / 10 [ 60%] (Sampling) Chain 4: Iteration: 7 / 10 [ 70%] (Sampling) Chain 4: Iteration: 8 / 10 [ 80%] (Sampling) Chain 4: Iteration: 9 / 10 [ 90%] (Sampling) Chain 4: Iteration: 10 / 10 [100%] (Sampling) Chain 4: Chain 4: Elapsed Time: 0.001 seconds (Warm-up) Chain 4: 0.002 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: 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: 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 0.000221 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.21 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 0.000113 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.13 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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 0.000111 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.11 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 0.000123 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.23 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: 0.002 seconds (Sampling) Chain 4: 0.006 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 9.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.96 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: Chain 2: Gradient evaluation took 6.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.64 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: 0.006 seconds (Sampling) Chain 2: 0.013 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 6.4e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.64 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: Chain 4: Gradient evaluation took 6.8e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.68 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 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 2.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.004 seconds (Sampling) Chain 2: 0.006 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 0.000166 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.66 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: Chain 2: Gradient evaluation took 0.000158 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.58 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 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: 0.005 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.006 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 3.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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: 0.012 seconds (Sampling) Chain 2: 0.013 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 0.000139 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.39 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: 0.006 seconds (Sampling) Chain 1: 0.015 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000126 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.002 seconds (Sampling) Chain 2: 0.009 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 3.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 2.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: 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: 0.001 seconds (Sampling) Chain 2: 0.003 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: Chain 1: Gradient evaluation took 0.000128 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.28 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: 0.005 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: Chain 2: Gradient evaluation took 0.000131 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.31 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: [ FAIL 5 | WARN 86 | 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 86 | SKIP 9 | PASS 75 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [20s/22s] 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 4.9e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.49 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: 0.004 seconds (Sampling) Chain 1: 0.007 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: 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: 0.004 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: 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: 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 9.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.93 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: 0.006 seconds (Sampling) Chain 2: 0.014 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 7.9e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.79 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: 0.006 seconds (Warm-up) Chain 1: 0.006 seconds (Sampling) Chain 1: 0.012 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 5.5e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds. Chain 2: Adjust your expectations accordingly! 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 1). Chain 1: Chain 1: Gradient evaluation took 3.1e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.002 seconds (Sampling) Chain 1: 0.003 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.6e-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: 0.002 seconds (Warm-up) Chain 2: 0.001 seconds (Sampling) Chain 2: 0.003 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000147 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.47 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: Chain 2: Gradient evaluation took 8.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.88 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: 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 4.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.006 seconds (Sampling) Chain 1: 0.01 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 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: 0.002 seconds (Warm-up) Chain 2: 0.001 seconds (Sampling) Chain 2: 0.003 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 0.00016 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.6 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: 0.009 seconds (Warm-up) Chain 1: 0.014 seconds (Sampling) Chain 1: 0.023 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: Chain 2: Gradient evaluation took 0.00011 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.1 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: 0.002 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 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 3.1e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 1.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 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: 0.001 seconds (Warm-up) Chain 2: 0.001 seconds (Sampling) Chain 2: 0.002 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 3.5e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.35 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: 0.001 seconds (Warm-up) Chain 3: 0.003 seconds (Sampling) Chain 3: 0.004 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 2.4e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.24 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: Chain 1: Gradient evaluation took 0.00011 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.1 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: 0.003 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: 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: 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 0.000109 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: 0.007 seconds (Warm-up) Chain 2: 0.005 seconds (Sampling) Chain 2: 0.012 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 9.3e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.93 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: 0.002 seconds (Sampling) Chain 3: 0.005 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: 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 8.9e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.89 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: 0.002 seconds (Sampling) Chain 4: 0.006 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 6.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.66 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 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: 0.005 seconds (Warm-up) Chain 2: 0.005 seconds (Sampling) Chain 2: 0.01 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 5.1e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.51 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 5.5e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.55 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: 0.003 seconds (Warm-up) Chain 4: 0.005 seconds (Sampling) Chain 4: 0.008 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 3.4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 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: 0.002 seconds (Warm-up) Chain 2: 0.003 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: 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 0.000104 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.04 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: 0.004 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: 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 8.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.86 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: 0.013 seconds (Sampling) Chain 2: 0.023 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 3.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 1.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: Chain 1: Gradient evaluation took 0.000114 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.14 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: 0.014 seconds (Sampling) Chain 1: 0.023 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 0.00011 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.1 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 4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 seconds (Sampling) Chain 1: 0.002 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 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: 0.001 seconds (Warm-up) Chain 2: 0 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: Chain 1: Gradient evaluation took 0.000112 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.12 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: 0.003 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.004 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 0.000116 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.16 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: 0.008 seconds (Warm-up) Chain 2: 0.01 seconds (Sampling) Chain 2: 0.018 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-debian-gcc

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’ [46s/50s] 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 4.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: Chain 2: Gradient evaluation took 3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.3 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: 0.004 seconds (Sampling) Chain 2: 0.005 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000222 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.22 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 0.000197 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.97 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: 0.003 seconds (Sampling) Chain 2: 0.011 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.00014 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.4 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 8.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.84 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 4.3e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.43 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: 0.001 seconds (Sampling) Chain 1: 0.004 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 4.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.43 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: 0.004 seconds (Sampling) Chain 2: 0.007 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000271 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.71 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: 0.008 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: 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 0.000223 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.23 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: 0.008 seconds (Warm-up) Chain 2: 0.003 seconds (Sampling) Chain 2: 0.011 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 5.4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: Chain 2: Gradient evaluation took 3.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.38 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: 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 0.000314 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.14 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 0.000226 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.26 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.003 seconds (Sampling) Chain 2: 0.009 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 3.9e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.39 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: Chain 2: Gradient evaluation took 3.5e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.35 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 3). Chain 3: Chain 3: Gradient evaluation took 3.6e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.36 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: 0.001 seconds (Sampling) Chain 3: 0.005 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 3.7e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.37 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: 0.003 seconds (Sampling) Chain 4: 0.01 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000232 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.32 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: 0.008 seconds (Sampling) Chain 1: 0.016 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: 0.008 seconds (Warm-up) Chain 2: 0.008 seconds (Sampling) Chain 2: 0.016 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 0.000218 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 2.18 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: 0.008 seconds (Sampling) Chain 3: 0.015 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: 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: 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: 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 0.000186 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.86 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 0.000114 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.14 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 8.7e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.87 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: 0.003 seconds (Sampling) Chain 2: 0.009 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 8.6e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.86 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 0.00012 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.2 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: 0.008 seconds (Sampling) Chain 4: 0.014 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 3.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.38 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: 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 0.000193 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.93 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: 0.009 seconds (Sampling) Chain 1: 0.016 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 0.000194 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.94 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 4.9e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.49 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: 0.007 seconds (Sampling) Chain 1: 0.01 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.4 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: 0.002 seconds (Sampling) Chain 2: 0.003 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 0.000328 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.28 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: 0.008 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: 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 0.000254 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.54 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: 0.007 seconds (Warm-up) Chain 2: 0.009 seconds (Sampling) Chain 2: 0.016 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: 0.008 seconds (Sampling) Chain 1: 0.009 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: 0.007 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: 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 0.000246 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.46 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: 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: 0.009 seconds (Sampling) Chain 1: 0.016 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000173 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.73 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: [ 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: tests
Result: ERROR Running 'testthat.R' [27s] 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 0.000116 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.16 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: 0.001 seconds (Sampling) Chain 1: 0.007 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds. 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: 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: 0.009 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.01 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 0.000166 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.66 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: 0.017 seconds (Warm-up) Chain 2: 0.015 seconds (Sampling) Chain 2: 0.032 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 5.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.58 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.014 seconds (Sampling) Chain 1: 0.023 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 5.7e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.57 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: 0.006 seconds (Sampling) Chain 2: 0.011 seconds (Total) Chain 2: 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: 0.004 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: Chain 2: Gradient evaluation took 2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: Chain 1: Gradient evaluation took 0.000142 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.011 seconds (Sampling) Chain 1: 0.021 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000132 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.32 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: 0.001 seconds (Sampling) Chain 2: 0.009 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 2.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.013 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.016 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.001 seconds (Sampling) Chain 2: 0.008 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 0.000165 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.65 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: 0.006 seconds (Sampling) Chain 1: 0.011 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 9.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.93 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: 0.011 seconds (Warm-up) Chain 2: 0.013 seconds (Sampling) Chain 2: 0.024 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 2.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.25 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: 0.001 seconds (Sampling) Chain 1: 0.01 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: 0.001 seconds (Sampling) Chain 2: 0.01 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 1.9e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: 0.001 seconds (Warm-up) Chain 3: 0.001 seconds (Sampling) Chain 3: 0.002 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 1.9e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds. Chain 4: Adjust your expectations accordingly! Chain 4: Chain 4: Chain 4: WARNING: No variance estimation is Chain 4: performed for num_warmup < 20 Chain 4: Chain 4: Iteration: 1 / 10 [ 10%] (Warmup) Chain 4: Iteration: 2 / 10 [ 20%] (Warmup) Chain 4: Iteration: 3 / 10 [ 30%] (Warmup) Chain 4: Iteration: 4 / 10 [ 40%] (Warmup) Chain 4: Iteration: 5 / 10 [ 50%] (Warmup) Chain 4: Iteration: 6 / 10 [ 60%] (Sampling) Chain 4: Iteration: 7 / 10 [ 70%] (Sampling) Chain 4: Iteration: 8 / 10 [ 80%] (Sampling) Chain 4: Iteration: 9 / 10 [ 90%] (Sampling) Chain 4: Iteration: 10 / 10 [100%] (Sampling) Chain 4: Chain 4: Elapsed Time: 0.001 seconds (Warm-up) Chain 4: 0 seconds (Sampling) Chain 4: 0.001 seconds (Total) Chain 4: 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 0.000157 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.57 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.007 seconds (Sampling) Chain 1: 0.013 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: 0.007 seconds (Warm-up) Chain 2: 0.007 seconds (Sampling) Chain 2: 0.014 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 0.000147 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.47 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: 0.002 seconds (Sampling) Chain 3: 0.009 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: 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: 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 0.000153 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.53 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: 0.011 seconds (Warm-up) Chain 4: 0.013 seconds (Sampling) Chain 4: 0.024 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 6.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.62 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: 0.001 seconds (Sampling) Chain 1: 0.007 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: 0.008 seconds (Warm-up) Chain 2: 0.01 seconds (Sampling) Chain 2: 0.018 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 3.6e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.36 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: 0.001 seconds (Sampling) Chain 3: 0.009 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 6e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.6 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: 0.013 seconds (Sampling) Chain 4: 0.022 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 3.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.007 seconds (Sampling) Chain 1: 0.016 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: 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: 0.008 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: 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 0.000137 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.37 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: 0.008 seconds (Warm-up) Chain 1: 0.002 seconds (Sampling) Chain 1: 0.01 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 0.000131 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.31 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: 0.011 seconds (Sampling) Chain 2: 0.019 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 1.9e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: 0.005 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.006 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 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: 0.005 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.007 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000157 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.57 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.012 seconds (Warm-up) Chain 1: 0.014 seconds (Sampling) Chain 1: 0.026 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 0.000151 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.51 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: 0.011 seconds (Warm-up) Chain 2: 0.012 seconds (Sampling) Chain 2: 0.023 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.017 seconds (Warm-up) Chain 2: 0.004 seconds (Sampling) Chain 2: 0.021 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 0.000162 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.62 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.001 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: Chain 2: Gradient evaluation took 0.000102 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.02 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: 0.019 seconds (Sampling) Chain 2: 0.027 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-windows-x86_64

Version: 1.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [32s/40s] 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 4.1e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.41 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: 0.007 seconds (Warm-up) Chain 1: 0.002 seconds (Sampling) Chain 1: 0.009 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 10 [ 10%] (Warmup) Chain 2: Iteration: 2 / 10 [ 20%] (Warmup) Chain 2: Iteration: 3 / 10 [ 30%] (Warmup) Chain 2: Iteration: 4 / 10 [ 40%] (Warmup) Chain 2: Iteration: 5 / 10 [ 50%] (Warmup) Chain 2: Iteration: 6 / 10 [ 60%] (Sampling) Chain 2: Iteration: 7 / 10 [ 70%] (Sampling) Chain 2: Iteration: 8 / 10 [ 80%] (Sampling) Chain 2: Iteration: 9 / 10 [ 90%] (Sampling) Chain 2: Iteration: 10 / 10 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 0.002 seconds (Warm-up) Chain 2: 0.001 seconds (Sampling) Chain 2: 0.003 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000173 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.73 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: Chain 2: Gradient evaluation took 0.000128 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 5.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.004 seconds (Sampling) Chain 1: 0.008 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 6.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.68 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 3.7e-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: 0.007 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.008 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 10 [ 10%] (Warmup) Chain 2: Iteration: 2 / 10 [ 20%] (Warmup) Chain 2: Iteration: 3 / 10 [ 30%] (Warmup) Chain 2: Iteration: 4 / 10 [ 40%] (Warmup) Chain 2: Iteration: 5 / 10 [ 50%] (Warmup) Chain 2: Iteration: 6 / 10 [ 60%] (Sampling) Chain 2: Iteration: 7 / 10 [ 70%] (Sampling) Chain 2: Iteration: 8 / 10 [ 80%] (Sampling) Chain 2: Iteration: 9 / 10 [ 90%] (Sampling) Chain 2: Iteration: 10 / 10 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 0.001 seconds (Warm-up) Chain 2: 0.007 seconds (Sampling) Chain 2: 0.008 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: 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 0.00016 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.6 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: 0.004 seconds (Warm-up) Chain 1: 0.003 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: Chain 2: Gradient evaluation took 0.000137 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.37 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: 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 3.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.003 seconds (Sampling) Chain 1: 0.006 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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: Chain 1: Gradient evaluation took 0.000151 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.51 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: 0.005 seconds (Warm-up) Chain 1: 0.004 seconds (Sampling) Chain 1: 0.009 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000134 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.34 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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 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 3.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.38 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 2.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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 3). Chain 3: Chain 3: Gradient evaluation took 3e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.3 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: 0.001 seconds (Sampling) Chain 3: 0.003 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 2.4e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.24 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: Chain 1: Gradient evaluation took 0.000147 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.47 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: 0.004 seconds (Sampling) Chain 1: 0.008 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.00011 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.1 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 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: Chain 3: Gradient evaluation took 9.4e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.94 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: Chain 4: Gradient evaluation took 9.9e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.99 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 7.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.78 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: 0.006 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 5.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.59 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 3). Chain 3: Chain 3: Gradient evaluation took 5.6e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.56 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: Chain 4: Gradient evaluation took 6.1e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.61 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: 0.003 seconds (Warm-up) Chain 4: 0.002 seconds (Sampling) Chain 4: 0.005 seconds (Total) Chain 4: 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: 0.003 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.006 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.001 seconds (Sampling) Chain 2: 0.003 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: Chain 1: Gradient evaluation took 0.000142 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.004 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: Chain 2: Gradient evaluation took 0.000114 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.14 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: 0.004 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.006 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: 0.002 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 2.7e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 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 0.000133 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: 0.003 seconds (Warm-up) Chain 1: 0.001 seconds (Sampling) Chain 1: 0.004 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 0.000119 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.19 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: 0.002 seconds (Warm-up) Chain 1: 0 seconds (Sampling) Chain 1: 0.002 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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: Chain 1: Gradient evaluation took 0.000115 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.15 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: Chain 2: Gradient evaluation took 0.00012 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.004 seconds (Sampling) Chain 2: 0.008 seconds (Total) Chain 2: [ FAIL 5 | WARN 86 | 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 86 | SKIP 9 | PASS 75 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 1.2.1
Check: tests
Result: ERROR Running ‘testthat.R’ [33s/40s] 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 4.6e-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: 0.007 seconds (Warm-up) Chain 1: 0.006 seconds (Sampling) Chain 1: 0.013 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 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: 0.003 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: Chain 2: Gradient evaluation took 0.00014 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.4 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 6.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.62 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: 0.003 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 6.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.64 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: 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: 0.004 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: Chain 2: Gradient evaluation took 2.1e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.21 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: 0.002 seconds (Warm-up) Chain 2: 0.003 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 0.000193 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.93 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: 0.012 seconds (Warm-up) Chain 1: 0.009 seconds (Sampling) Chain 1: 0.021 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 0.000122 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.22 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: 0.004 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.006 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 3.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.005 seconds (Sampling) Chain 1: 0.007 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.007 seconds (Sampling) Chain 2: 0.008 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: 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 0.000136 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.36 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 10 [ 10%] (Warmup) Chain 1: Iteration: 2 / 10 [ 20%] (Warmup) Chain 1: Iteration: 3 / 10 [ 30%] (Warmup) Chain 1: Iteration: 4 / 10 [ 40%] (Warmup) Chain 1: Iteration: 5 / 10 [ 50%] (Warmup) Chain 1: Iteration: 6 / 10 [ 60%] (Sampling) Chain 1: Iteration: 7 / 10 [ 70%] (Sampling) Chain 1: Iteration: 8 / 10 [ 80%] (Sampling) Chain 1: Iteration: 9 / 10 [ 90%] (Sampling) Chain 1: Iteration: 10 / 10 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.008 seconds (Warm-up) Chain 1: 0.008 seconds (Sampling) Chain 1: 0.016 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000153 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.53 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: 0.004 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.006 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 3.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.001 seconds (Sampling) Chain 1: 0.004 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: 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: 0.004 seconds (Sampling) Chain 2: 0.007 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 2.2e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds. Chain 3: Adjust your expectations accordingly! 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: 0.001 seconds (Warm-up) Chain 3: 0.001 seconds (Sampling) Chain 3: 0.002 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 2.2e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds. Chain 4: Adjust your expectations accordingly! Chain 4: Chain 4: Chain 4: WARNING: No variance estimation is Chain 4: performed for num_warmup < 20 Chain 4: Chain 4: Iteration: 1 / 10 [ 10%] (Warmup) Chain 4: Iteration: 2 / 10 [ 20%] (Warmup) Chain 4: Iteration: 3 / 10 [ 30%] (Warmup) Chain 4: Iteration: 4 / 10 [ 40%] (Warmup) Chain 4: Iteration: 5 / 10 [ 50%] (Warmup) Chain 4: Iteration: 6 / 10 [ 60%] (Sampling) Chain 4: Iteration: 7 / 10 [ 70%] (Sampling) Chain 4: Iteration: 8 / 10 [ 80%] (Sampling) Chain 4: Iteration: 9 / 10 [ 90%] (Sampling) Chain 4: Iteration: 10 / 10 [100%] (Sampling) Chain 4: Chain 4: Elapsed Time: 0.002 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: 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: 0.009 seconds (Warm-up) Chain 1: 0.013 seconds (Sampling) Chain 1: 0.022 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000149 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.49 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: 0.008 seconds (Warm-up) Chain 2: 0.009 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: Chain 3: Gradient evaluation took 0.000123 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.23 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: Chain 4: Gradient evaluation took 0.000131 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.31 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: 0.004 seconds (Sampling) Chain 4: 0.008 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 6.9e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 6.6e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.66 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 6.3e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.63 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 6.5e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.65 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: 0.005 seconds (Warm-up) Chain 4: 0.005 seconds (Sampling) Chain 4: 0.01 seconds (Total) Chain 4: 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: 0.003 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 3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.3 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: 0.001 seconds (Sampling) Chain 2: 0.003 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 0.000155 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.55 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 0.000136 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.36 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: 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: 0.001 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 2.2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 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: 0.002 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: Chain 1: Gradient evaluation took 0.000127 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.27 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 0.000117 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.17 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: 0.004 seconds (Warm-up) Chain 2: 0.004 seconds (Sampling) Chain 2: 0.008 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: 0.007 seconds (Warm-up) Chain 1: 0 seconds (Sampling) Chain 1: 0.007 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.3 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: 0.002 seconds (Sampling) Chain 2: 0.008 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: Chain 1: Gradient evaluation took 0.000341 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.41 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: 0.003 seconds (Warm-up) Chain 1: 0.004 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: 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: 0.003 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.005 seconds (Total) Chain 2: [ FAIL 5 | WARN 86 | 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 86 | SKIP 9 | PASS 75 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 1.2.1
Check: tests
Result: ERROR Running 'testthat.R' [28s] 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 0.000168 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.68 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: 0.001 seconds (Sampling) Chain 1: 0.008 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: Chain 1: Gradient evaluation took 0.000175 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.75 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: 0.01 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: 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 9.7e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.97 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: 0.011 seconds (Warm-up) Chain 2: 0.012 seconds (Sampling) Chain 2: 0.023 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 6.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.66 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: 0.002 seconds (Sampling) Chain 1: 0.011 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 6.1e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.61 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: 0.012 seconds (Warm-up) Chain 2: 0.014 seconds (Sampling) Chain 2: 0.026 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 2.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 2.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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: 0.013 seconds (Warm-up) Chain 2: 0.001 seconds (Sampling) Chain 2: 0.014 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: Chain 1: Gradient evaluation took 0.000161 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.61 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: 0.002 seconds (Sampling) Chain 1: 0.008 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000102 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.02 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: 0.013 seconds (Sampling) Chain 2: 0.019 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 2.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.006 seconds (Sampling) Chain 1: 0.012 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: 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: 0.014 seconds (Warm-up) Chain 2: 0.011 seconds (Sampling) Chain 2: 0.025 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 0.000189 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.89 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.008 seconds (Sampling) Chain 1: 0.013 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000148 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.48 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: 0.002 seconds (Sampling) Chain 2: 0.011 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 2.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.002 seconds (Sampling) Chain 1: 0.003 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.4e-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 3). Chain 3: Chain 3: Gradient evaluation took 1.3e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.13 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: 0.001 seconds (Warm-up) Chain 3: 0.001 seconds (Sampling) Chain 3: 0.002 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 1.4e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.14 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: 0.008 seconds (Warm-up) Chain 4: 0.003 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 0.000178 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: 0.008 seconds (Warm-up) Chain 1: 0.002 seconds (Sampling) Chain 1: 0.01 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 0.000119 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.19 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: 0.013 seconds (Sampling) Chain 2: 0.022 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: Chain 3: Gradient evaluation took 0.00015 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.5 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: 0.002 seconds (Sampling) Chain 3: 0.01 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: 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: 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 0.000149 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.49 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: 0.008 seconds (Warm-up) Chain 4: 0.011 seconds (Sampling) Chain 4: 0.019 seconds (Total) Chain 4: 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: 0.012 seconds (Sampling) Chain 1: 0.022 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 6.5e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.65 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: 0.007 seconds (Sampling) Chain 2: 0.017 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 4.4e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.44 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: 0.012 seconds (Sampling) Chain 3: 0.019 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 6.6e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.66 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: 0.008 seconds (Warm-up) Chain 4: 0.007 seconds (Sampling) Chain 4: 0.015 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 2.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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 seconds (Sampling) Chain 1: 0.007 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 1.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 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: 0.016 seconds (Warm-up) Chain 2: 0.004 seconds (Sampling) Chain 2: 0.02 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 0.000116 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.16 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: 0.008 seconds (Sampling) Chain 1: 0.014 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: Chain 2: Gradient evaluation took 0.000156 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.56 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: 0.01 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.012 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 2.3e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.23 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: 0.001 seconds (Sampling) Chain 1: 0.006 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.1e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.21 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: 0.003 seconds (Warm-up) Chain 2: 0.005 seconds (Sampling) Chain 2: 0.008 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: Chain 1: Gradient evaluation took 0.000152 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.52 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: 0.011 seconds (Warm-up) Chain 1: 0.011 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: Chain 2: Gradient evaluation took 0.000154 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.54 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: 0.008 seconds (Warm-up) Chain 2: 0.01 seconds (Sampling) Chain 2: 0.018 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.007 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.009 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 0.000163 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.63 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: 0.012 seconds (Sampling) Chain 1: 0.02 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 0.00018 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.8 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.013 seconds (Warm-up) Chain 2: 0.013 seconds (Sampling) Chain 2: 0.026 seconds (Total) Chain 2: [ FAIL 5 | WARN 84 | 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 84 | SKIP 9 | PASS 75 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

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

Version: 1.2.1
Check: tests
Result: ERROR Running 'testthat.R' [37s] 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 0.000202 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.02 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: 0.009 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.012 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: 0.019 seconds (Warm-up) Chain 2: 0.003 seconds (Sampling) Chain 2: 0.022 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 0.000315 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.15 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: 0.012 seconds (Warm-up) Chain 1: 0.017 seconds (Sampling) Chain 1: 0.029 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000286 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.86 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: 0.014 seconds (Warm-up) Chain 2: 0.017 seconds (Sampling) Chain 2: 0.031 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000142 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.011 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.014 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: 0.011 seconds (Warm-up) Chain 2: 0.017 seconds (Sampling) Chain 2: 0.028 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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 3.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.39 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: 0.011 seconds (Warm-up) Chain 2: 0.002 seconds (Sampling) Chain 2: 0.013 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000281 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.81 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: 0.013 seconds (Warm-up) Chain 1: 0.017 seconds (Sampling) Chain 1: 0.03 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 0.000277 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.77 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: 0.002 seconds (Sampling) Chain 2: 0.012 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 2.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.001 seconds (Sampling) Chain 1: 0.008 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 10 [ 10%] (Warmup) Chain 2: Iteration: 2 / 10 [ 20%] (Warmup) Chain 2: Iteration: 3 / 10 [ 30%] (Warmup) Chain 2: Iteration: 4 / 10 [ 40%] (Warmup) Chain 2: Iteration: 5 / 10 [ 50%] (Warmup) Chain 2: Iteration: 6 / 10 [ 60%] (Sampling) Chain 2: Iteration: 7 / 10 [ 70%] (Sampling) Chain 2: Iteration: 8 / 10 [ 80%] (Sampling) Chain 2: Iteration: 9 / 10 [ 90%] (Sampling) Chain 2: Iteration: 10 / 10 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 0.006 seconds (Warm-up) Chain 2: 0.005 seconds (Sampling) Chain 2: 0.011 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: Chain 1: Gradient evaluation took 0.000224 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.24 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: 0.011 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.014 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 0.000306 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.06 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: 0.012 seconds (Warm-up) Chain 2: 0.018 seconds (Sampling) Chain 2: 0.03 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 2.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: 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: 0.004 seconds (Sampling) Chain 1: 0.009 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 2.5e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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 3). Chain 3: Chain 3: Gradient evaluation took 2.6e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: WARNING: 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: 0.001 seconds (Warm-up) Chain 3: 0.009 seconds (Sampling) Chain 3: 0.01 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 2.3e-05 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.23 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: 0.005 seconds (Warm-up) Chain 4: 0.001 seconds (Sampling) Chain 4: 0.006 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000257 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.57 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: 0.012 seconds (Warm-up) Chain 1: 0.003 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: 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 0.00022 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.2 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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: 0.015 seconds (Warm-up) Chain 2: 0.017 seconds (Sampling) Chain 2: 0.032 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 0.000207 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 2.07 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: 0.002 seconds (Sampling) Chain 3: 0.009 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 0.000147 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.47 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: 0.012 seconds (Warm-up) Chain 4: 0.017 seconds (Sampling) Chain 4: 0.029 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000104 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.04 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: 0.011 seconds (Warm-up) Chain 1: 0.015 seconds (Sampling) Chain 1: 0.026 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.000117 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.17 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: 0.007 seconds (Warm-up) Chain 2: 0.001 seconds (Sampling) Chain 2: 0.008 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 6.5e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.65 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: 0.013 seconds (Warm-up) Chain 3: 0.017 seconds (Sampling) Chain 3: 0.03 seconds (Total) Chain 3: SAMPLING FOR MODEL 'TK' NOW (CHAIN 4). Chain 4: Chain 4: Gradient evaluation took 0.000119 seconds Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.19 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: 0.011 seconds (Warm-up) Chain 4: 0.017 seconds (Sampling) Chain 4: 0.028 seconds (Total) Chain 4: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 2.7e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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 2.7e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: WARNING: No variance estimation is Chain 2: performed for num_warmup < 20 Chain 2: Chain 2: Iteration: 1 / 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 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: Chain 1: Gradient evaluation took 0.000222 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.22 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: No variance estimation is Chain 1: performed for num_warmup < 20 Chain 1: Chain 1: Iteration: 1 / 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: 0.012 seconds (Warm-up) Chain 1: 0.003 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: 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 0.00021 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.1 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: 0.014 seconds (Warm-up) Chain 2: 0.016 seconds (Sampling) Chain 2: 0.03 seconds (Total) Chain 2: SAMPLING FOR MODEL 'TK' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 5.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.52 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: WARNING: 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: 0.016 seconds (Warm-up) Chain 1: 0.01 seconds (Sampling) Chain 1: 0.026 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.4 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: 0.001 seconds (Sampling) Chain 2: 0.011 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 0.000305 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.05 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: 0.011 seconds (Warm-up) Chain 1: 0.003 seconds (Sampling) Chain 1: 0.014 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: Chain 2: Gradient evaluation took 0.000311 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.11 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: 0.013 seconds (Warm-up) Chain 2: 0.018 seconds (Sampling) Chain 2: 0.031 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: 0.002 seconds (Sampling) Chain 1: 0.003 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 4.4e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.44 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: 0.012 seconds (Sampling) Chain 2: 0.014 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 0.000376 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.76 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: 0.015 seconds (Warm-up) Chain 1: 0.018 seconds (Sampling) Chain 1: 0.033 seconds (Total) Chain 1: SAMPLING FOR MODEL 'TK' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 0.00037 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 3.7 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: 0.016 seconds (Warm-up) Chain 2: 0.017 seconds (Sampling) Chain 2: 0.033 seconds (Total) Chain 2: [ FAIL 5 | WARN 85 | 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 85 | SKIP 9 | PASS 75 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64