* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/AnimalAPD.Rcheck’
* using R Under development (unstable) (2021-09-20 r80940)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AnimalAPD/DESCRIPTION’ ... OK
* this is package ‘AnimalAPD’ version ‘1.0.0’
* 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 ‘AnimalAPD’ can be installed ... [14s/14s] OK
* checking package 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 R 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 ... 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 ... [21s/21s] 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 examples ... OK
* checking examples with --run-donttest ... [58s/58s] ERROR
Running examples in ‘AnimalAPD-Ex.R’ failed
The error most likely occurred in:

> ### Name: APDRE
> ### Title: Activity Probability Density Controlling for Random Effects
> ### Aliases: APDRE
> ### Keywords: Bayesian activity; cameratrap; temporal;
> 
> ### ** Examples
> 
> data(wolfexample)
> data(boarexample)
> ## No test: 
>  APDRE(focal=wolfexample$Radians, contingent=boarexample$Radians, 
+     RE1=wolfexample$SamplingPeriod, weibullGLMM=TRUE, frechetGLMM=FALSE,
+     gammaGLMM=FALSE, lognormalGLMM=FALSE, invgaussianGLMM=FALSE,
+     min=TRUE, max=TRUE, points=TRUE, mean=TRUE, HDI=TRUE, rawmean=FALSE) 
---------------------
Running Weibull model
  
Compiling Stan program...
Start sampling

SAMPLING FOR MODEL '42bbdb5012c648a368a07e72623aeb2a' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
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Chain 1: Iteration: 5000 / 5000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.868306 seconds (Warm-up)
Chain 1:                0.755767 seconds (Sampling)
Chain 1:                1.62407 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL '42bbdb5012c648a368a07e72623aeb2a' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 0 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 5000 [  0%]  (Warmup)
Chain 2: Iteration:  500 / 5000 [ 10%]  (Warmup)
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Chain 2: Iteration: 4500 / 5000 [ 90%]  (Sampling)
Chain 2: Iteration: 5000 / 5000 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.798479 seconds (Warm-up)
Chain 2:                0.960986 seconds (Sampling)
Chain 2:                1.75947 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL '42bbdb5012c648a368a07e72623aeb2a' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 0 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 5000 [  0%]  (Warmup)
Chain 3: Iteration:  500 / 5000 [ 10%]  (Warmup)
Chain 3: Iteration: 1000 / 5000 [ 20%]  (Warmup)
Chain 3: Iteration: 1500 / 5000 [ 30%]  (Warmup)
Chain 3: Iteration: 2000 / 5000 [ 40%]  (Warmup)
Chain 3: Iteration: 2500 / 5000 [ 50%]  (Warmup)
Chain 3: Iteration: 2501 / 5000 [ 50%]  (Sampling)
Chain 3: Iteration: 3000 / 5000 [ 60%]  (Sampling)
Chain 3: Iteration: 3500 / 5000 [ 70%]  (Sampling)
Chain 3: Iteration: 4000 / 5000 [ 80%]  (Sampling)
Chain 3: Iteration: 4500 / 5000 [ 90%]  (Sampling)
Chain 3: Iteration: 5000 / 5000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0.820484 seconds (Warm-up)
Chain 3:                1.19836 seconds (Sampling)
Chain 3:                2.01884 seconds (Total)
Chain 3: 

All MCMC chains reached convergence (rhat<1.05)


All MCMC chains achieved the minimum effective sample size. Minimum ESS = 5370

Error in round(c(summ$random$RE1[1, 1], summ$random$RE1[1, 3:4]), 3) : 
  non-numeric argument to mathematical function
Calls: APDRE
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/AnimalAPD.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:42.97, 150.36 + 11.81