Running examples in 'beautier-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_scale_param
> ### Title: Create a parameter called scale
> ### Aliases: create_scale_param create_param_scale
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> # Create the parameter
> scale_param <- create_scale_param()
> 
> # Use the parameter in a distribution
> laplace_distr <- create_laplace_distr(
+   scale = scale_param
+ )
> 
> # Use the distribution to create a BEAST2 input file
> beast2_input_file <- get_beautier_tempfilename()
> create_beast2_input_file(
+   input_filename = get_fasta_filename(),
+   beast2_input_file,
+   tree_prior = create_yule_tree_prior(
+     birth_rate_distr = laplace_distr
+   )
+ )
Killed
Found the following HTML validation problems:
create_treelog_xml.html:19:1: Warning: missing </h2> before <pre>
create_treelog_xml.html:25:7: Warning: discarding unexpected </h2>
Running examples in ‘beautier-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_test_ns_mcmc
> ### Title: Create an NS MCMC object for testing
> ### Aliases: create_test_ns_mcmc
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> mcmc <- create_test_ns_mcmc()
> beast2_input_file <- get_beautier_tempfilename()
> create_beast2_input_file(
+   get_fasta_filename(),
+   beast2_input_file,
+   mcmc = mcmc
+ )

Execution halted
Running examples in ‘beautier-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_test_inference_model
> ### Title: Create a testing inference model.
> ### Aliases: create_test_inference_model
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> inference_model <- create_test_inference_model()
> 
> beast2_input_file <- get_beautier_tempfilename()
> create_beast2_input_file_from_model(
+   get_fasta_filename(),
+   beast2_input_file,
+   inference_model = inference_model
+ )

Execution halted
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> check_empty_beautier_folder()
> 
>  # <distribution id="posterior" spec="util.CompoundDistribution">
>  #     <distribution id="prior" spec="util.CompoundDistribution">
>  #       HERE, where the ID of the distribution is 'prior'
>  #     </distribution>
>  #     <distribution id="likelihood" ...>
>  #     </distribution>
>  # </distribution>
> 
> check_empty_beautier_folder()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1724.96 71.86 1803.39 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running examples in ‘beautier-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_strict_clock_model
> ### Title: Create a strict clock model
> ### Aliases: create_strict_clock_model create_clock_model_strict
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> strict_clock_model <- create_strict_clock_model(
+   clock_rate_param = 1.0,
+   clock_rate_distr = create_uniform_distr()
+ )
> 
> beast2_input_file <- get_beautier_tempfilename()
> create_beast2_input_file(
+   get_fasta_filename(),
+   beast2_input_file,
+   clock_model = strict_clock_model
+ )
> file.remove(beast2_input_file)
[1] TRUE
> 
> strict_clock_model_gamma <- create_strict_clock_model(
+   clock_rate_distr = create_gamma_distr()
+ )
> 
> beast2_input_file <- get_beautier_tempfilename()
> create_beast2_input_file(
+   get_fasta_filename(),
+   beast2_input_file,
+   clock_model = strict_clock_model_gamma
+ )
Killed
Running examples in ‘beautier-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_site_model
> ### Title: General function to create a site model.
> ### Aliases: create_site_model
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> input_filename <- get_fasta_filename()
> gtr_site_model <- create_gtr_site_model()
> hk_site_model <- create_hky_site_model()
> jc69_site_model <- create_jc69_site_model()
> tn93_site_model <- create_tn93_site_model()
> 
> # Can use any site model
> output_filename <- get_beautier_tempfilename()
> create_beast2_input_file(
+   input_filename = input_filename,
+   output_filename = output_filename,
+   site_model = jc69_site_model
+ )
Killed
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> is_rate_ac_param(create_rate_ag_param())
[1] FALSE
> is_rate_ac_param(create_rate_at_param())
[1] FALSE
> is_rate_ac_param(create_rate_cg_param())
[1] FALSE
> is_rate_ac_param(create_rate_ct_param())
[1] FALSE
> is_rate_ac_param(create_rate_gt_param())
[1] FALSE
> is_rate_ac_param(create_s_param())
[1] FALSE
> is_rate_ac_param(create_scale_param())
[1] FALSE
> is_rate_ac_param(create_sigma_param())
[1] FALSE
> 
> is_rate_ac_param(NA)
[1] FALSE
> is_rate_ac_param(NULL)
[1] FALSE
> is_rate_ac_param("nonsense")
[1] FALSE
> is_rate_ac_param(create_jc69_site_model())
[1] FALSE
> is_rate_ac_param(create_strict_clock_model())
[1] FALSE
> is_rate_ac_param(create_yule_tree_prior())
[1] FALSE
> is_rate_ac_param(create_mcmc())
======== End of example output (where/before crash/hang up occured ?) ========
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ### Name: create_test_ns_inference_model
> ### Title: Create an inference model to be tested by Nested Sampling
> ### Aliases: create_test_ns_inference_model
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> inference_model <- create_test_ns_inference_model()
> 
> check_empty_beautier_folder()
> 
> 
> 
> cleanEx()
> nameEx("create_test_ns_mcmc")
> ### * create_test_ns_mcmc
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: create_test_ns_mcmc
> ### Title: Create an NS MCMC object for testing
> ### Aliases: create_test_ns_mcmc
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
> 
> mcmc <- create_test_ns_mcmc()
======== End of example output (where/before crash/hang up occured ?) ========