* using log directory ‘/srv/hornik/tmp/CRAN_pretest/DAISIEprep.Rcheck’
* using R Under development (unstable) (2025-10-01 r88895)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘DAISIEprep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAISIEprep’ version ‘1.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/10s] NOTE
Maintainer: ‘Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>’

New maintainer:
  Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Old maintainer(s):
  Joshua W. Lambert <j.w.l.lambert@rug.nl>
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘DAISIEprep’ can be installed ... [3s/3s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [5s/5s] OK
* checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [50s/50s] ERROR
  Running ‘testthat.R’ [50s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DAISIEprep)
  > 
  > test_check("DAISIEprep")
  Don't know how to automatically pick scale for object of type <formula>. Defaulting to continuous.
  Don't know how to automatically pick scale for object of type <formula>. Defaulting to continuous.
  Don't know how to automatically pick scale for object of type <formula>. Defaulting to continuous.
  Don't know how to automatically pick scale for object of type <formula>. Defaulting to continuous.
  [ FAIL 4 | WARN 0 | SKIP 14 | PASS 2237 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • Run only on CI (3): 'test-sensitivity.R:2:3', 'test-sensitivity.R:40:3',
    'test-sensitivity.R:78:3'
  • empty test (11): 'test-create_daisie_data.R:169:1',
    'test-create_daisie_data.R:173:1', 'test-create_daisie_data.R:177:1',
    'test-create_daisie_data.R:181:1', 'test-create_daisie_data.R:185:1',
    'test-create_daisie_data.R:189:1', 'test-create_daisie_data.R:231:1',
    'test-create_daisie_data.R:235:1', 'test-create_daisie_data.R:239:1',
    'test-create_daisie_data.R:243:1', 'test-create_daisie_data.R:247:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plot_phylod.R:5:3'): plot_phylod runs silent without error ───
  `tree <- plot_phylod(phylod = phylod, node_pies = FALSE)` did not throw the expected warning.
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-plot_phylod.R:5:3
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::expect_warning(...)
  ── Failure ('test-plot_phylod.R:16:3'): plot_phylod runs silent without error ──
  `tree <- plot_phylod(phylod = phylod, node_pies = FALSE)` did not throw the expected warning.
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-plot_phylod.R:16:3
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::expect_warning(...)
  ── Error ('test-plot_phylod.R:27:3'): plot_phylod runs silent without error ────
  Error in `geom_bar(stat = "identity", alpha = alpha, color = outline.color, 
      size = outline.size, show.legend = F)`: Problem while computing aesthetics.
  i Error occurred in the 1st layer.
  Caused by error:
  ! Aesthetics are not valid data columns.
  x The following aesthetics are invalid:
  * `y = y`
  * `fill = fill`
  i Did you mistype the name of a data column or forget to add `after_stat()`?
  ── Error ('test-plot_phylod.R:38:3'): plot_phylod runs silent without error ────
  Error in `geom_bar(stat = "identity", alpha = alpha, color = outline.color, 
      size = outline.size, show.legend = F)`: Problem while computing aesthetics.
  i Error occurred in the 1st layer.
  Caused by error:
  ! Aesthetics are not valid data columns.
  x The following aesthetics are invalid:
  * `y = y`
  * `fill = fill`
  i Did you mistype the name of a data column or forget to add `after_stat()`?
  
  [ FAIL 4 | WARN 0 | SKIP 14 | PASS 2237 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [38s/38s] OK
* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE