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Type 'q()' to quit R. > # 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) > > 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 output file: report.knit.md "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc22ef078602ccc.html --lua-filter "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "D:\RCompile\CRANpkg\lib\4.6\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css "D:/RCompile/CRANincoming/R-devel/lib/OmicFlow/styles.css" --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "D:\temp\2025_08_18_13_30_17_17029\RtmpQzwuq6\rmarkdown-str22ef03e142568.html" Output created: report.html 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 0 | WARN 0 | SKIP 9 | PASS 3 ] ══ 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' [ FAIL 0 | WARN 0 | SKIP 9 | PASS 3 ] > > proc.time() user system elapsed 10.53 1.14 12.48