- using R version 4.5.1 (2025-06-13)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-19) 14.2.0
GNU Fortran (Debian 14.2.0-19) 14.2.0
- running under: Debian GNU/Linux 13 (trixie)
- using session charset: UTF-8
- checking for file ‘rbioacc/DESCRIPTION’ ... OK
- this is package ‘rbioacc’ version ‘1.2.1’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘rbioacc’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
- checking C++ specification ... OK
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [4s/5s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the package can be unloaded cleanly ... [4s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the namespace can be unloaded cleanly ... [4s/6s] OK
- checking loading without being on the library search path ... [7s/9s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [23s/28s] OK
- checking Rd files ... [0s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in shell scripts ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [8s/9s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [33s/41s] 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:
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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!
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Chain 2: performed for num_warmup < 20
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[ 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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [37s/45s] OK
- checking PDF version of manual ... [6s/8s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR