• using R Under development (unstable) (2025-08-09 r88544)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 ... [13m/33m] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
• checking C++ specification ... OK
• checking package directory ... 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... [12s/16s] 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 ... [37s/54s] OK
• checking Rd files ... 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 ... 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 ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [50s/62s] ERROR   Running ‘testthat.R’ [49s/61s] 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 5.6e-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: 0.003 seconds (Warm-up)   Chain 1: 0.006 seconds (Sampling)   Chain 1: 0.009 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: 0.002 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: 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 0.000253 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.53 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 0.000227 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.27 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: 0.006 seconds (Warm-up)   Chain 2: 0.003 seconds (Sampling)   Chain 2: 0.009 seconds (Total)   Chain 2:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 0.000145 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.45 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: 0.008 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 0.000189 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.89 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: 0.01 seconds (Sampling)   Chain 2: 0.019 seconds (Total)   Chain 2:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 5e-05 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.5 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 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:   Chain 1: Gradient evaluation took 0.000223 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.23 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: 0.006 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:   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: 0.005 seconds (Warm-up)   Chain 2: 0.003 seconds (Sampling)   Chain 2: 0.008 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 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: 0.002 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 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: 0.004 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 0.000334 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.34 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: 0.01 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: 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: 0.008 seconds (Warm-up)   Chain 2: 0.005 seconds (Sampling)   Chain 2: 0.013 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 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: 0.002 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 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: 0.003 seconds (Warm-up)   Chain 2: 0.015 seconds (Sampling)   Chain 2: 0.018 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: 0.002 seconds (Warm-up)   Chain 3: 0.005 seconds (Sampling)   Chain 3: 0.007 seconds (Total)   Chain 3:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).   Chain 4:   Chain 4: Gradient evaluation took 4.7e-05 seconds   Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.47 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: 0.002 seconds (Warm-up)   Chain 4: 0.004 seconds (Sampling)   Chain 4: 0.006 seconds (Total)   Chain 4:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 0.000207 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.07 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: 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 0.000216 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.16 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: 0.009 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:   Chain 3: Gradient evaluation took 0.000234 seconds   Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 2.34 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: 0.014 seconds (Warm-up)   Chain 3: 0.014 seconds (Sampling)   Chain 3: 0.028 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 0.000228 seconds   Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 2.28 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: 0.003 seconds (Sampling)   Chain 4: 0.015 seconds (Total)   Chain 4:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 8e-05 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.8 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: 0.003 seconds (Sampling)   Chain 1: 0.01 seconds (Total)   Chain 1:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).   Chain 2:   Chain 2: Gradient evaluation took 0.000103 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.03 seconds.   Chain 2: Adjust your expectations accordingly!   Chain 2:   Chain 2:   Chain 2: WARNING: No variance estimation is   Chain 2: performed for num_warmup < 20   Chain 2:   Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)   Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)   Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)   Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)   Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)   Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)   Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)   Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)   Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)   Chain 2: Iteration: 10 / 10 [100%] (Sampling)   Chain 2:   Chain 2: Elapsed Time: 0.007 seconds (Warm-up)   Chain 2: 0.008 seconds (Sampling)   Chain 2: 0.015 seconds (Total)   Chain 2:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).   Chain 3:   Chain 3: Gradient evaluation took 0.000127 seconds   Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.27 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:   Chain 4: Gradient evaluation took 9.1e-05 seconds   Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.91 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: 0.016 seconds (Warm-up)   Chain 4: 0.022 seconds (Sampling)   Chain 4: 0.038 seconds (Total)   Chain 4:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   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: 0.002 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 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: 0.001 seconds (Sampling)   Chain 2: 0.002 seconds (Total)   Chain 2:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 0.000329 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.29 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: 0.012 seconds (Warm-up)   Chain 1: 0.013 seconds (Sampling)   Chain 1: 0.025 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 0.000267 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.67 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: 0.009 seconds (Warm-up)   Chain 2: 0.01 seconds (Sampling)   Chain 2: 0.019 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: 0.006 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: 0.005 seconds (Warm-up)   Chain 2: 0.003 seconds (Sampling)   Chain 2: 0.008 seconds (Total)   Chain 2:      SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).   Chain 1:   Chain 1: Gradient evaluation took 0.000218 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.18 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: 0.011 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: 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 0.000203 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.03 seconds.   Chain 2: Adjust your expectations accordingly!   Chain 2:   Chain 2:   Chain 2: WARNING: No variance estimation is   Chain 2: performed for num_warmup < 20   Chain 2:   Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)   Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)   Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)   Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)   Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)   Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)   Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)   Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)   Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)   Chain 2: Iteration: 10 / 10 [100%] (Sampling)   Chain 2:   Chain 2: Elapsed Time: 0.012 seconds (Warm-up)   Chain 2: 0.011 seconds (Sampling)   Chain 2: 0.023 seconds (Total)   Chain 2:      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: 0.003 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 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: 0.003 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:   Chain 1: Gradient evaluation took 0.00023 seconds   Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.3 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: 0.009 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 0.000216 seconds   Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.16 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: 0.018 seconds (Warm-up)   Chain 2: 0.007 seconds (Sampling)   Chain 2: 0.025 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [67s/89s] OK
• checking PDF version of manual ... [10s/18s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR