* using log directory 'd:/Rcompile/CRANpkg/local/4.4/MiscMetabar.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MiscMetabar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MiscMetabar' version '0.14.3'
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MiscMetabar' can be installed ... OK
* checking installed package size ... 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 ... [20s] OK
* checking whether the package can be loaded with stated dependencies ... [19s] OK
* checking whether the package can be unloaded cleanly ... [21s] OK
* checking whether the namespace can be loaded with stated dependencies ... [20s] OK
* checking whether the namespace can be unloaded cleanly ... [22s] OK
* checking loading without being on the library search path ... [22s] 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 ... [59s] OK
* checking Rd files ... [15s] OK
* checking Rd metadata ... 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 ... [11s] 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 ... [334s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [84s] ERROR
  Running 'spelling.R' [0s]
  Running 'testthat.R' [83s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MiscMetabar)
  Loading required package: phyloseq
  Loading required package: ggplot2
  Loading required package: dada2
  Loading required package: Rcpp
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: purrr
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:testthat':
  
      is_null
  
  > 
  > test_check("MiscMetabar")
  Starting 2 test processes
  [ FAIL 1 | WARN 2 | SKIP 75 | PASS 81 ]
  
  ══ Skipped tests (75) ══════════════════════════════════════════════════════════
  • On CRAN (63): 'test_adonis.R:1:1', 'test_controls.R:7:3',
    'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
    'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
    'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
    'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
    'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
    'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
    'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
    'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',
    'test_figures_biplot.R:52:3', 'test_figures_misc.R:26:3',
    'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:9:3',
    'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
    'test_figures_beta_div.R:22:3', 'test_figures_beta_div.R:73:5',
    'test_figures_beta_div.R:92:3', 'test_figures_beta_div.R:102:5',
    'test_figures_beta_div.R:159:5', 'test_figures_beta_div.R:241:5',
    'test_figures_beta_div.R:259:5', 'test_figures_beta_div.R:289:5',
    'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',
    'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',
    'test_krona.R:7:3', 'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
    'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
    'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
    'test_figures_taxo.R:379:3', 'test_phyloseq_class.R:10:3',
    'test_phyloseq_class.R:51:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
    'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:34:5',
    'test_table_functions.R:47:5', 'test_targets.R:5:3', 'test_targets.R:56:3',
    'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
    'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
    'test_misc.R:30:3', 'test_misc.R:97:3'
  • On Windows (12): 'test_figures_misc.R:10:3', 'test_figures_misc.R:18:3',
    'test_figures_beta_div.R:208:3', 'test_figures_beta_div.R:401:3',
    'test_figures_beta_div.R:413:3', 'test_figures_taxo.R:413:3',
    'test_phyloseq_class.R:93:3', 'test_rw.R:38:3', 'test_table_functions.R:5:3',
    'test_table_functions.R:18:3', 'test_targets.R:83:3', 'test_targets.R:128:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────
  `graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.
  
  [ FAIL 1 | WARN 2 | SKIP 75 | PASS 81 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [33s] OK
* checking PDF version of manual ... [27s] OK
* checking HTML version of manual ... [31s] OK
* DONE
Status: 1 ERROR