* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/bite.Rcheck’
* using R Under development (unstable) (2024-08-09 r86986)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘bite/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bite’ version ‘0.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘mvMORPH’
* 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 ‘bite’ can be installed ... [20s/25s] 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 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 ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [33s/33s] 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 data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘bite-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_jive
> ### Title: Create a list that can be used as an input to mcmc_bite
> ### Aliases: make_jive
> 
> ### ** Examples
> 
> 
> ## Load test data
> data(Anolis_traits)
> data(Anolis_tree)
> data(Anolis_map)
> 
> ## JIVE object to run jive with single regimes
> my.jive <- make_jive(phy = Anolis_tree, traits = Anolis_traits[,-3],
+  model.priors = list(mean = "BM", logvar= c("OU", "root")))
mean prior model: BM [1]
logvar prior model: OU + root [1]
> 
> ## JIVE object to run jive with multiple regimes
> my.jive <- make_jive(Anolis_tree, Anolis_traits[,-3], map = Anolis_map,
+  model.priors =list(mean = "BM", logvar = c("OU", "theta", "alpha")))
mean prior model: BM [1]
logvar prior model: OU + theta + alpha [2]
> 
> ## JIVE object to run jive from an ancestral state reconstruction (stochastic mapping)
> # First generate simmap object
> library(phytools)
Loading required package: ape
Loading required package: maps
> n= length(Anolis_tree$tip.label)
> trait = rep(0,n)
> trait[c(4,3,14,16, 6,5)] = 1
> names(trait) =  Anolis_tree$tip.label
> 
> mapped_tree=make.simmap(Anolis_tree, trait, model='SYM')
make.simmap is sampling character histories conditioned on
the transition matrix

Q =
            0           1
0 -0.01156974  0.01156974
1  0.01156974 -0.01156974
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
  0   1 
0.5 0.5 
Done.
> plotSimmap(mapped_tree)
no colors provided. using the following legend:
        0         1 
  "black" "#DF536B" 
> 
> my.jive <- make_jive(mapped_tree, Anolis_traits[,-3]
+ , model.priors = list(mean = "OU" , logvar = c("OU", "theta")))
mean prior model: OU [1]
logvar prior model: OU + theta [2]
>  
>  ## Jive object using another model of trait evolution (EB from mvMORPH)
>  library(mvMORPH)
Error in library(mvMORPH) : there is no package called ‘mvMORPH’
Execution halted
* checking PDF version of manual ... 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, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/bite.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:39.94, 136.99 + 14.38