* using log directory 'd:/Rcompile/CRANpkg/local/4.4/betaper.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'betaper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'betaper' version '1.1-2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
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* checking for portable file names ... OK
* checking whether package 'betaper' can be installed ... OK
* checking installed package size ... 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 ... [2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s] OK
* checking loading without being on the library search path ... [2s] OK
* checking use of S3 registration ... 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 ... [8s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 ... [1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [5s] 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
> 
> Amazonia4.p2 <- pertables.p2(Amazonia[1:50,], index=index.Amazon, nsim=4, ncl=2, iseed=4)
> set.seed(2)
> Amazonia.adonis <- adonis_pertables(Amazonia4.p2  ~ Ca + K + Mg + Na, data=soils)
Error in adonis(formula = fmla, data = data, permutations = permutations,  : 
  'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis_pertables -> adonis -> .Defunct
Execution halted
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 1 ERROR