* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/treestats.Rcheck’
* using R Under development (unstable) (2025-11-06 r88990)
* 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 ‘treestats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treestats’ version ‘1.70.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘abcrf’
* 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 ‘treestats’ can be installed ... [198s/85s] OK
* used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* checking C++ specification ... 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 ... [11s/11s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘treestats-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_unbalanced_tree
> ### Title: Stepwise increase the imbalance of a tree
> ### Aliases: make_unbalanced_tree
> 
> ### ** Examples
> 
> simulated_tree <- ape::rphylo(n = 16, birth = 1, death = 0)
> balanced_tree <- treestats::create_fully_balanced_tree(simulated_tree)
> unbalanced_tree <- treestats::create_fully_unbalanced_tree(simulated_tree)
> intermediate_tree <- make_unbalanced_tree(balanced_tree, 8)
Error in loadNamespace(x) : there is no package called ‘DDD’
Calls: make_unbalanced_tree ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(treestats) # nolint keep package name non-all-lowercase, due to backwards compatibility
  Loading required package: Rcpp
  > 
  > test_check("treestats")
  Failed with error:  'there is no package called 'phyloTop''
  Failed with error:  'there is no package called 'phyloTop''
  Failed with error:  'there is no package called 'apTreeshape''
  Failed with error:  'there is no package called 'phyloTop''
  Failed with error:  'there is no package called 'apTreeshape''
  Failed with error:  'there is no package called 'adephylo''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'castor''
  Failed with error:  'there is no package called 'picante''
  Failed with error:  'there is no package called 'geiger''
  Failed with error:  'there is no package called 'geiger''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'Matrix''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'phyloTop''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'RSpectra''
  Failed with error:  'there is no package called 'igraph''
  Failed with error:  'there is no package called 'picante''
  Failed with error:  'there is no package called 'picante''
  Failed with error:  'there is no package called 'DDD''
  Failed with error:  'there is no package called 'geiger''
  Failed with error:  'there is no package called 'phyloTop''
  Failed with error:  'there is no package called 'picante''
  Failed with error:  'there is no package called 'apTreeshape''
  Failed with error:  'there is no package called 'phyloTop''
  Failed with error:  'there is no package called 'phyloTop''
  [ FAIL 5 | WARN 0 | SKIP 25 | PASS 579 ]
  
  ══ Skipped tests (25) ══════════════════════════════════════════════════════════
  • On CRAN (6): 'test-allstats.R:4:3', 'test-brts_stats.R:4:3',
    'test-colless_corr.R:33:3', 'test-colless_quad.R:33:3', 'test-rpanda.R:4:3',
    'test-topology_stats.R:4:3'
  • empty test (18): 'test-ILnumber.R:3:1', 'test-avgLadder.R:3:1',
    'test-beta.R:3:1', 'test-cherries.R:3:1', 'test-colless.R:3:1',
    'test-crown_age.R:3:1', 'test-gamma.R:5:1', 'test-j.R:3:1',
    'test-l2phylo.R:3:1', 'test-l2phylo.R:51:1', 'test-max_betweenness.R:51:1',
    'test-max_ladder.R:3:1', 'test-minmax_laplace.R:67:1', 'test-mpd.R:3:1',
    'test-pitchforks.R:3:1', 'test-psv.R:3:1', 'test-stairs.R:3:1',
    'test-stairs.R:26:1'
  • {lintr} is not installed (1): 'test-style.R:2:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-make_unbalanced_tree.R:12:7'): usage ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'DDD'
  Backtrace:
      ▆
   1. ├─treestats::make_unbalanced_tree(...) at test-make_unbalanced_tree.R:12:7
   2. │ └─treestats:::make_any(ltab_in, unbal_steps, selection_method)
   3. │   └─treestats:::make_unbalanced_tree_random(ltab_in, unbal_steps)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-minmax_adj.R:27:3'): usage ─────────────────────────────────────
  Error in `eval(code, test_env)`: object 'focal_tree' not found
  Backtrace:
      ▆
   1. └─treestats::minmax_adj(focal_tree, use_rspectra = FALSE) at test-minmax_adj.R:27:3
   2.   └─treestats:::check_tree(...)
  ── Error ('test-nltt.R:9:3'): usage ────────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'nLTT'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-nltt.R:9:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-phylo2l.R:7:3'): usage ─────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'DDD'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-phylo2l.R:7:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-treeness.R:7:3'): usage ────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'DDD'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-treeness.R:7:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 5 | WARN 0 | SKIP 25 | PASS 579 ]
  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 ... 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/treestats.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:40.59, 246.33 + 22.70