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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 ] 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 8 | PASS 2 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): '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 8 | PASS 2 ] > > proc.time() user system elapsed 7.26 1.03 7.96