* using log directory ‘/srv/hornik/tmp/CRAN/diversitree.Rcheck’
* using R Under development (unstable) (2023-12-02 r85657)
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    Debian clang version 17.0.5 (1)
    Debian flang-new version 17.0.5 (1)
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* this is package ‘diversitree’ version ‘0.9-21’
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Maintainer: ‘Richard G. FitzJohn <rich.fitzjohn@gmail.com>’
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* checking examples ... [2s/2s] ERROR
Running examples in ‘diversitree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make.bisse
> ### Title: Binary State Speciation and Extinction Model
> ### Aliases: make.bisse starting.point.bisse
> ### Keywords: models
> 
> ### ** Examples
> 
> ## Due to a change in sample() behaviour in newer R it is necessary to
> ## use an older algorithm to replicate the previous examples
> if (getRversion() >= "3.6.0") {
+   RNGkind(sample.kind = "Rounding")
+ }
Warning in RNGkind(sample.kind = "Rounding") :
  non-uniform 'Rounding' sampler used
> pars <- c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01)
> set.seed(4)
> phy <- tree.bisse(pars, max.t=30, x0=0)
> 
> ## Here is the 52 species tree with the true character history coded.
> ## Red is state '1', which has twice the speciation rate of black (state
> ## '0').
> h <- history.from.sim.discrete(phy, 0:1)
> plot(h, phy)
> 
> lik <- make.bisse(phy, phy$tip.state)
> lik(pars) # -159.71
[1] -159.71
> 
> ## Heuristic guess at a starting point, based on the constant-rate
> ## birth-death model (uses make.bd).
> p <- starting.point.bisse(phy)
> 
> ## Not run: 
> ##D ## Start an ML search from this point.  This takes some time (~7s)
> ##D fit <- find.mle(lik, p, method="subplex")
> ##D logLik(fit) # -158.6875
> ##D 
> ##D ## The estimated parameters aren't too far away from the real ones, even
> ##D ## with such a small tree
> ##D rbind(real=pars,
> ##D       estimated=round(coef(fit), 2))
> ##D 
> ##D ## Test a constrained model where the speciation rates are set equal
> ##D ## (takes ~4s).
> ##D lik.l <- constrain(lik, lambda1 ~ lambda0)
> ##D fit.l <- find.mle(lik.l, p[-1], method="subplex")
> ##D logLik(fit.l) # -158.7357
> ##D 
> ##D ## Despite the difference in the estimated parameters, there is no
> ##D ## statistical support for this difference:
> ##D anova(fit, equal.lambda=fit.l)
> ##D 
> ##D ## Run an MCMC.  Because we are fitting six parameters to a tree with
> ##D ## only 50 species, priors will be needed.  I will use an exponential
> ##D ## prior with rate 1/(2r), where r is the character independent
> ##D ## diversificiation rate:
> ##D prior <- make.prior.exponential(1 / (2 * (p[1] - p[3])))
> ##D 
> ##D ## This takes quite a while to run, so is not run by default
> ##D tmp <- mcmc(lik, fit$par, nsteps=100, prior=prior, w=.1, print.every=0)
> ##D 
> ##D w <- diff(sapply(tmp[2:7], range))
> ##D samples <- mcmc(lik, fit$par, nsteps=1000, prior=prior, w=w,
> ##D                 print.every=100)
> ##D 
> ##D ## See profiles.plot for more information on plotting these
> ##D ## profiles.
> ##D col <- c("blue", "red")
> ##D profiles.plot(samples[c("lambda0", "lambda1")], col.line=col, las=1,
> ##D               xlab="Speciation rate", legend="topright")
> ## End(Not run)
> 
> ## BiSSE reduces to the birth-death model and Mk2 when diversification
> ## is state independent (i.e., lambda0 ~ lambda1 and mu0 ~ mu1).
> lik.mk2 <- make.mk2(phy, phy$tip.state)
> lik.bd <- make.bd(phy)
> 
> ## 1. BiSSE / Birth-Death
> ## Set the q01 and q10 parameters to arbitrary numbers (need not be
> ## symmetric), and constrain the lambdas and mus to be the same for each
> ## state.  The likelihood function now has just two parameters and
> ## will be proprtional to Nee's birth-death based likelihood:
> lik.bisse.bd <- constrain(lik,
+                           lambda1 ~ lambda0, mu1 ~ mu0,
+                           q01 ~ .01, q10 ~ .02)
> pars <- c(.1, .03)
> ## These differ by -167.3861 for both parameter sets:
> lik.bisse.bd(pars)   - lik.bd(pars)
[1] -167.3861
> lik.bisse.bd(2*pars) - lik.bd(2*pars)
[1] -167.3861
> 
> ## 2. BiSSE / Mk2
> ## Same idea as above: set all diversification parameters to arbitrary
> ## values (but symmetric this time):
> lik.bisse.mk2 <- constrain(lik,
+                            lambda0 ~ .1, lambda1 ~ .1,
+                            mu0 ~ .03, mu1 ~ .03)
> ## Differ by -150.4740 for both parameter sets.
> lik.bisse.mk2(pars)   - lik.mk2(pars)
[1] -150.474
> lik.bisse.mk2(2*pars) - lik.mk2(2*pars)
[1] -150.474
> 
> ## 3. Sampled BiSSE / Birth-Death
> ## Pretend that the tree is only .6 sampled:
> lik.bd2 <- make.bd(phy, sampling.f=.6)
> lik.bisse2 <- make.bisse(phy, phy$tip.state, sampling.f=c(.6, .6))
> lik.bisse2.bd <- constrain(lik.bisse2,
+                            lambda1 ~ lambda0, mu1 ~ mu0,
+                            q01 ~ .01, q10 ~ .01)
> 
> ## Difference of -167.2876
> lik.bisse2.bd(pars)   - lik.bd2(pars)
[1] -167.2876
> lik.bisse2.bd(2*pars) - lik.bd2(2*pars)
[1] -167.2876
> 
> ## 4. Unresolved clade BiSSE / Birth-Death
> unresolved <- data.frame(tip.label=I(c("sp25", "sp30", "sp40", "sp56", "sp20")),
+                          Nc =c(10, 9, 6, 5, 2),
+                          n0=0, n1=0)
> unresolved.bd <- structure(unresolved$Nc, names=unresolved$tip.label)
> lik.bisse3 <- make.bisse(phy, phy$tip.state, unresolved)
> lik.bisse3.bd <- constrain(lik.bisse3,
+                            lambda1 ~ lambda0, mu1 ~ mu0,
+                            q01 ~ .01, q10 ~ .01)
> lik.bd3 <- make.bd(phy, unresolved=unresolved.bd)
> 
> ## Difference of -167.1523
> lik.bisse3.bd(pars) - lik.bd3(pars)
Error: segfault from C stack overflow
Execution halted
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR