- using R version 4.5.1 (2025-06-13)
- using platform: x86_64-pc-linux-gnu
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gcc-14 (Debian 14.2.0-19) 14.2.0
GNU Fortran (Debian 14.2.0-19) 14.2.0
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See the install log for details.
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- checking examples ... [2s/6s] ERROR
Running examples in ‘betaper-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
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- DONE
Status: 1 ERROR