Last updated on 2026-06-07 02:50:32 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 387.70 | 202.75 | 590.45 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 314.25 | 173.94 | 488.19 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 398.00 | 322.06 | 720.06 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 840.00 | 392.25 | 1232.25 | OK | |
| r-devel-windows-x86_64 | 1.3.1 | 407.00 | 248.00 | 655.00 | OK | |
| r-patched-linux-x86_64 | 1.3.1 | 380.50 | 229.78 | 610.28 | OK | |
| r-release-linux-x86_64 | 1.3.1 | 387.53 | 228.24 | 615.77 | OK | |
| r-release-macos-arm64 | 1.3.1 | 73.00 | 7.00 | 80.00 | OK | |
| r-release-macos-x86_64 | 1.3.1 | 238.00 | 168.00 | 406.00 | OK | |
| r-release-windows-x86_64 | 1.3.1 | 396.00 | 253.00 | 649.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.1 | 306.00 | 168.00 | 474.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.1 | 513.00 | 322.00 | 835.00 | OK |
Version: 1.3.1
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 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: 0.013 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.021 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: 0.008 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.99 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 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:
Chain 2: Gradient evaluation took 6.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.69 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 3.9e-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: 0.004 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 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: 0.005 seconds (Warm-up)
Chain 2: 0.005 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''
Saving _problems/test-data-3.R
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: 0.005 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 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: 0.002 seconds (Warm-up)
Chain 2: 0.005 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:
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: 0.004 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.004212 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 42.12 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 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:
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 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: 0.004 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 1.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.15 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 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 1.1e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.11 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: 0.001 seconds (Sampling)
Chain 4: 0.002 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 7.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.71 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 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:
Chain 2: Gradient evaluation took 6.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.67 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: 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 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: 0.003 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 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)
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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:
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SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds.
Chain 2: Adjust your expectations accordingly!
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SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.1e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
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SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.7e-05 seconds
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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.
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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.
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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.
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Chain 1: Gradient evaluation took 9.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.98 seconds.
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Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
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Chain 2: Gradient evaluation took 6.5e-05 seconds
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[ FAIL 1 | WARN 33 | SKIP 6 | PASS 72 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• 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:69:3', 'test-predict_manual.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data.R:3:3'): data load no complain ────────────────────────────
Error in `file(file, if (append) "a" else "w")`: cannot open the connection
Backtrace:
▆
1. └─testthat::expect_silent(data("Male_Gammarus_Single")) at test-data.R:3:3
2. └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. └─testthat (local) .capture(...)
4. └─withr::with_output_sink(...)
5. └─withr:::set_output_sink(file = new, append = append, split = split)
6. └─withr:::output_sink(file = file, append = append, split = split)
7. └─base::sink(file = file, append = append, type = "output", split = split)
8. └─base::file(file, if (append) "a" else "w")
[ FAIL 1 | WARN 33 | SKIP 6 | PASS 72 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc