* using log directory 'd:/Rcompile/CRANpkg/local/3.5/betaper.Rcheck'
* using R version 3.5.3 (2019-03-11)
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* this is package 'betaper' version '1.1-1'
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* checking examples ... ERROR
Running examples in 'betaper-Ex.R' failed
The error most likely occurred in:

> ### Name: adonis_pertables
> ### Title: Function to assess the efects of taxonomic uncertainty on
> ###   permutational multivariate analysis of variance using distance
> ###   matrices
> ### Aliases: adonis_pertables print.adonis_pertables plot.adonis_pertables
> ### Keywords: multivariate
> 
> ### ** Examples
> 
>  
> 
> 
> data(Amazonia)
> data(soils)
> 
> # Define a new index that includes the terms used in the \code{Amazonia} dataset to define
> # undetermined taxa at different taxonomic levels
> 
> index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")
> 
> # Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic
> # uncertainty)
>  ## Not run: 
> ##D Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)
> ##D 
> ##D # Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test:
> ##D 
> ##D Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)
> ##D 
> ##D Amazonia.adonis
> ##D 
> ##D plot(Amazonia.adonis)
> ## End(Not run)
> # Fast example for Rcheck
> 
> Amazonia_subset <- Amazonia[1:50,]
> Amazonia4.p2<- pertables.p2(Amazonia_subset, index=index.Amazon, nsim=4, ncl=2)
> 
> Amazonia.adonis <- adonis_pertables(Amazonia4.p2  ~ Ca + K + Mg + Na, data=soils)
> 
> Amazonia.adonis
Permutation tests for multivariate analysis of variance using distance matrices 

Call:
adonis_pertables(formula = Amazonia4.p2 ~ Ca + K + Mg + Na, data = soils) 

Permutation: free
Number of permutations: 5

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model      R2  Pr(>F) Pr(tax)    
Ca         1   0.40368 0.40368  1.3171 0.13150 0.33333  <2e-16 ***
K          1   0.71782 0.71782  2.3420 0.23382 0.16667  <2e-16 ***
Mg         1   0.31974 0.31974  1.0432 0.10415 0.33333     0.2    
Na         1   0.40264 0.40264  1.3137 0.13116 0.16667  <2e-16 ***
Residuals  4   1.22602 0.30650         0.39937                    
Total      8   3.06990                 1.00000                    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1


Confidence intervals of R-squared under different taxonomic scenarios 

              Ca         K         Mg        Na
0%    0.09882812 0.1530674 0.08828236 0.1013104
0.5%  0.09901019 0.1532109 0.08838444 0.1014249
2.5%  0.09973847 0.1537845 0.08879274 0.1018827
50%   0.11846149 0.1631589 0.10286023 0.1090655
97.5% 0.14542299 0.2154916 0.12441948 0.1095191
99.5% 0.14668566 0.2188518 0.12531374 0.1095405
100%  0.14700133 0.2196919 0.12553730 0.1095459


Confidence intervals of p-values under different taxonomic scenarios 

             Ca         K        Mg        Na
0%    0.3333333 0.1666667 0.3333333 0.3333333
0.5%  0.3358333 0.1666667 0.3383333 0.3383333
2.5%  0.3458333 0.1666667 0.3583333 0.3583333
50%   0.5833333 0.1666667 0.6666667 0.7500000
97.5% 0.8208333 0.1666667 0.8208333 0.8333333
99.5% 0.8308333 0.1666667 0.8308333 0.8333333
100%  0.8333333 0.1666667 0.8333333 0.8333333
> 
> plot(Amazonia.adonis)
Error in hist.default(z, plot = FALSE, breaks = seq(min(z), max(z), by = diff.z/30)) : 
  invalid number of 'breaks'
Calls: plot -> plot.adonis_pertables -> hist -> hist.default
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR