* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/phylospatial.Rcheck’
* using R Under development (unstable) (2025-11-24 r89055)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘phylospatial/DESCRIPTION’ ... OK
* this is package ‘phylospatial’ version ‘1.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘tmap’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phylospatial’ can be installed ... [5s/11s] OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [9s/15s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘phylospatial-Ex.R’ failed
The error most likely occurred in:

> ### Name: clade_dist
> ### Title: Pairwise distances among clades or nodes
> ### Aliases: clade_dist
> 
> ### ** Examples
> 
> clade_dist(ape::rtree(10))
Error in loadNamespace(x) : there is no package called ‘phytools’
Calls: clade_dist ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [129s/207s]
 [129s/208s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(phylospatial)
  > 
  > test_check("phylospatial")
  `phylospatial` object
    - 18 lineages across 400 sites
    - community data type: probability 
    - spatial data class: SpatRaster 
    - dissimilarity data: none 
  Community data type detected: probability
  Community data type detected: probability
  Community data type detected: probability
  Community data type detected: probability
  Raster data has no CRS, so can't check that cells are equal-area; it will be assumed that they are.
  Community data type detected: probability
  Loading required namespace: canaper
  Failed with error:  'there is no package called 'canaper''
  Community data type detected: abundance
  Saving _problems/test-ps_diversity-9.R
  Saving _problems/test-ps_diversity-10.R
  Saving _problems/test-ps_diversity-11.R
  Saving _problems/test-ps_diversity-12.R
  Saving _problems/test-ps_diversity-20.R
  Loading required namespace: furrr
  Failed with error:  'there is no package called 'furrr''
  Raster data has no CRS, so can't check that cells are equal-area; it will be assumed that they are.
  Community data type detected: probability
  Loading required namespace: furrr
  Failed with error:  'there is no package called 'furrr''
  [ FAIL 5 | WARN 1 | SKIP 6 | PASS 62 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-ps_diversity.R:3:7'
  • empty test (1): 'test-ps_canape.R:1:1'
  • {betapart} is not installed. (2): 'test-ps_dissim.R:17:7',
    'test-ps_dissim.R:30:7'
  • {hillR} is not installed. (1): 'test-ps_diversity.R:55:7'
  • {picante} is not installed. (1): 'test-ps_diversity.R:74:7'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-ps_diversity.R:9:7'): ps_diversity runs without error on simulated data of various types ──
  Expected `ps_diversity(ps_simulate(data_type = "probability"), "all")` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'phytools'
  ── Failure ('test-ps_diversity.R:10:7'): ps_diversity runs without error on simulated data of various types ──
  Expected `ps_diversity(ps_simulate(data_type = "binary"), "all")` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'phytools'
  ── Failure ('test-ps_diversity.R:11:7'): ps_diversity runs without error on simulated data of various types ──
  Expected `ps_diversity(ps_simulate(data_type = "abundance"), "all")` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'phytools'
  ── Failure ('test-ps_diversity.R:12:7'): ps_diversity runs without error on simulated data of various types ──
  Expected `ps_diversity(ps_simulate(spatial_type = "none"), "all")` not to throw any errors.
  Actually got a <packageNotFoundError> with message:
    there is no package called 'phytools'
  ── Error ('test-ps_diversity.R:20:7'): diversity measures match canaper, for binary data ──
  Error: Package `canaper` must be installed to use this function.
  Backtrace:
      ▆
   1. └─phylospatial::ps_canaper(ps, n_reps = 3, n_iterations = 3, spatial = FALSE) at test-ps_diversity.R:20:7
  
  [ FAIL 5 | WARN 1 | SKIP 6 | PASS 62 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [8s/12s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/phylospatial.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:44.96, 189.91 + 9.79