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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 Attaching package: 'data.table' The following object is masked from 'package:base': %notin% 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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. -- object metaData: 9 variables x 4 samples countData: 4 samples x 25 features featureData: 7 attributes x 25 features treeData: 25 tips x 24 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 63 features featureData: 7 attributes x 63 features treeData: 63 tips x 62 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 64 features featureData: 7 attributes x 64 features treeData: 64 tips x 63 nodes v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v countData is loaded. ! Created placeholder featureData. v treeData is loaded. -- object metaData: 2 variables x 10 samples countData: 10 samples x 50 features featureData: 0 attributes x 50 features treeData: 50 tips x 49 nodes i Processing ... column: CONTRAST_treatment -- object metaData: 2 variables x 10 samples countData: 10 samples x 50 features featureData: 0 attributes x 50 features treeData: 50 tips x 49 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 63 features featureData: 7 attributes x 63 features treeData: 63 tips x 62 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 63 features featureData: 7 attributes x 63 features treeData: 63 tips x 62 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v countData is loaded. ! Created placeholder featureData. v treeData is loaded. -- object metaData: 2 variables x 10 samples countData: 10 samples x 50 features featureData: 0 attributes x 50 features treeData: 50 tips x 49 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v countData is loaded. ! Created placeholder featureData. -- object metaData: 2 variables x 10 samples countData: 10 samples x 50 features featureData: 0 attributes x 50 features 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v featureData is loaded. v countData is loaded. v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v featureData is loaded. v countData is loaded. v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v countData is loaded. ! Created placeholder featureData. v metaData template passed the JSON validation. i Checking for duplicated identifiers .. v countData is loaded. ! Created placeholder featureData. 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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 countData is loaded. ! Created placeholder featureData. v treeData is loaded. -- object metaData: 2 variables x 10 samples countData: 10 samples x 50 features featureData: 0 attributes x 50 features treeData: 50 tips x 49 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. -- object metaData: 2 variables x 10 samples countData: 10 samples x 50 features featureData: 0 attributes x 50 features treeData: 50 tips x 49 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 185 features featureData: 7 attributes x 185 features treeData: 185 tips x 184 nodes -- object metaData: 9 variables x 2 samples countData: 2 samples x 115 features featureData: 7 attributes x 115 features treeData: 115 tips x 114 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 200 features featureData: 7 attributes x 200 features treeData: 200 tips x 199 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 50 features featureData: 7 attributes x 50 features treeData: 50 tips x 49 nodes v metaData template passed the JSON validation. i Checking for duplicated identifiers .. ! Placeholder featureData created. -- object metaData: 1 variables x 5 samples countData: 5 samples x 100 features featureData: 0 attributes x 100 features v metaData template passed the JSON validation. i Checking for duplicated identifiers .. -- object metaData: 1 variables x 5 samples featureData: 0 attributes x 100 features -- object metaData: 1 variables x 5 samples countData: 5 samples x 100 features featureData: 0 attributes x 100 features 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 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 -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes -- object metaData: 9 variables x 4 samples countData: 4 samples x 242 features featureData: 7 attributes x 242 features treeData: 242 tips x 241 nodes [ FAIL 0 | WARN 0 | SKIP 15 | PASS 6 ] ══ Skipped tests (15) ══════════════════════════════════════════════════════════ • On CRAN (14): 'test-alpha_diversity.R:1:1', 'test-composition.R:1:1', 'test-distances.R:1:1', 'test-distances.R:80:1', 'test-hill.R:1:1', 'test-hill.R:17:1', 'test-metagenomics.R:1:1', 'test-omics.R:1:1', 'test-ordination.R:1:1', 'test-proteomics.R:1:1', 'test-subsetting.R:1:1', 'test-sync.R:1:1', 'test-transformations.R:1:1', 'test-utils.R:1:1' • grepl("devel", R.version$status) is TRUE (1): 'test-dfe.R:18:3' [ FAIL 0 | WARN 0 | SKIP 15 | PASS 6 ] > > proc.time() user system elapsed 22.93 3.42 25.64