Last updated on 2026-07-23 20:51:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.9 | 28.20 | 245.32 | 273.52 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.9 | 17.92 | 146.84 | 164.76 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.9 | 50.00 | 278.76 | 328.76 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.9 | 21.00 | 153.65 | 174.65 | WARN | |
| r-devel-windows-x86_64 | 1.9 | 35.00 | 222.00 | 257.00 | OK | |
| r-patched-linux-x86_64 | 1.9 | 29.60 | 219.61 | 249.21 | OK | |
| r-release-linux-x86_64 | 1.9 | 25.59 | 218.28 | 243.87 | OK | |
| r-release-macos-arm64 | 1.9 | 7.00 | 47.00 | 54.00 | OK | |
| r-release-macos-x86_64 | 1.9 | 22.00 | 214.00 | 236.00 | OK | |
| r-release-windows-x86_64 | 1.9 | 39.00 | 222.00 | 261.00 | OK | |
| r-oldrel-macos-arm64 | 1.9 | OK | ||||
| r-oldrel-macos-x86_64 | 1.9 | 18.00 | 203.00 | 221.00 | OK | |
| r-oldrel-windows-x86_64 | 1.9 | 49.00 | 287.00 | 336.00 | OK |
Version: 1.9
Check: examples
Result: ERROR
Running examples in ‘dispRity-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis.dispRity
> ### Title: adonis dispRity (from 'vegan::adonis2')
> ### Aliases: adonis.dispRity
>
> ### ** Examples
>
> ## Adonis with one groups
>
> ## Generating a random character matrix
> character_matrix <- sim.morpho(rtree(20), 50, rates = c(rnorm, 1, 0))
> ## Calculating the distance matrix
> distance_matrix <- as.matrix(dist(character_matrix))
> ## Creating two groups
> random_groups <- list("group1" = 1:10, "group2" = 11:20)
>
> ## Generating a dispRity object
> random_disparity <- custom.subsets(distance_matrix, random_groups)
Warning: custom.subsets is applied on what seems to be a distance matrix.
The resulting matrices won't be distance matrices anymore!
You can use dist.data = TRUE, if you want to keep the data as a distance matrix.
> ## Running a default NPMANOVA
> adonis.dispRity(random_disparity)
Permutation test for adonis under reduced model
Permutation: free
Number of permutations: 999
vegan::adonis2(formula = matrix ~ group, method = "euclidean")
Df SumOfSqs R2 F Pr(>F)
Model 1 14.2 0.06443 1.2396 0.166
Residual 18 206.2 0.93557
Total 19 220.4 1.00000
>
>
> ## Adonis with multiple groups
>
> ## Creating a random matrix
> random_matrix <- matrix(data = rnorm(90), nrow = 10,
+ dimnames = list(letters[1:10]))
> ## Creating two groups with two states each
> groups <- as.data.frame(matrix(data = c(rep(1,5), rep(2,5), rep(c(1,2), 5)),
+ nrow = 10, ncol = 2, dimnames = list(letters[1:10], c("g1", "g2"))))
>
> ## Creating the dispRity object
> multi_groups <- custom.subsets(random_matrix, groups)
>
> ## Running the NPMANOVA
> adonis.dispRity(multi_groups, matrix ~ g1 + g2)
Warning in adonis.dispRity(multi_groups, matrix ~ g1 + g2) :
The input data for adonis.dispRity was not a distance matrix.
The results are thus based on the distance matrix for the input data (i.e. dist(data$matrix[[1]])).
Make sure that this is the desired methodological approach!
Permutation test for adonis under reduced model
Permutation: free
Number of permutations: 999
vegan::adonis2(formula = dist(matrix) ~ g1 + g2, method = "euclidean")
Df SumOfSqs R2 F Pr(>F)
Model 2 21.461 0.26492 1.2614 0.252
Residual 7 59.546 0.73508
Total 9 81.007 1.00000
>
> ## Adonis with time
>
> ## Creating time series
> data(BeckLee_mat50)
> data(BeckLee_tree)
> data(BeckLee_ages)
> time_subsets <- chrono.subsets(BeckLee_mat50, BeckLee_tree,
+ method = "discrete", inc.nodes = FALSE, time = c(100, 85, 65, 0),
+ FADLAD = BeckLee_ages)
>
> ## Running the NPMANOVA with time as a predictor
> adonis.dispRity(time_subsets, matrix ~ time)
Permutation test for adonis under reduced model
Permutation: free
Number of permutations: 999
vegan::adonis2(formula = dist(matrix) ~ time, method = "euclidean")
Df SumOfSqs R2 F Pr(>F)
Model 2 9.593 0.07769 1.9796 0.001 ***
Residual 47 113.884 0.92231
Total 49 123.477 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Warning message:
In adonis.dispRity(time_subsets, matrix ~ time) :*** buffer overflow detected ***: terminated
Aborted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.9
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
char.diff.c:27:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
See ‘/data/localhost/ripley/R/packages/tests-devel/dispRity.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
Flavor: r-devel-linux-x86_64-fedora-gcc