* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmicFlow.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88798)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.3.0-5) 14.3.0
    GNU Fortran (Debian 14.3.0-5) 14.3.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘OmicFlow/DESCRIPTION’ ... OK
* this is package ‘OmicFlow’ version ‘1.3.1’
* 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 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 ‘OmicFlow’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/OmicFlow-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the package can be unloaded cleanly ... [4s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/6s] OK
* checking loading without being on the library search path ... [4s/5s] 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 ... [20s/26s] OK
* checking Rd files ... [1s/1s] 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 examples ... [12s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [20s/27s] ERROR
  Running ‘testthat.R’ [20s/27s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(ggplot2)
  > library(OmicFlow)
  Loading required package: R6
  Loading required package: data.table
  Loading required package: Matrix
  > library(patchwork)
  > set.seed(100)
  > test_check("OmicFlow")
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  i Processing ... column: CONTRAST_sex 
  'nperm' >= set of all permutations: complete enumeration.
  Set of permutations < 'minperm'. Generating entire set.
  'nperm' >= set of all permutations: complete enumeration.
  Set of permutations < 'minperm'. Generating entire set.
  
  
  processing file: report.Rmd
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  'nperm' >= set of all permutations: complete enumeration.
  Set of permutations < 'minperm'. Generating entire set.
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
    'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
    'test-ordination.R:17:3', 'test-subsetting.R:10:3',
    'test-transformations.R:10:3', 'test-utils.R:15:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
   2. │ └─base::withCallingHandlers(...)
   3. └─taxa$autoFlow(filename = output_file)
   4.   └─rmarkdown::render(...)
   5.     └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   6.       └─xfun::write_utf8(res, output)
   7.         └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
   8.           └─base::file(con, "w")
  
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [7s/9s] OK
* checking HTML version of manual ... [1s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR