CRAN Package Check Results for Package OmicFlow

Last updated on 2025-09-02 20:51:43 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-gcc	1.3.0	10.90	94.42	105.32	ERROR
r-devel-linux-x86_64-fedora-clang	1.3.0			248.72	OK
r-devel-linux-x86_64-fedora-gcc	1.3.0			243.99	OK
r-release-macos-x86_64	1.3.0			130.00	OK
r-release-windows-x86_64	1.3.0	19.00	154.00	173.00	OK
r-oldrel-macos-x86_64	1.3.0			129.00	OK

Check Details

Version: 1.3.0
Check: tests
Result: ERROR Running ‘testthat.R’ [13s/15s] 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) > > 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 Flavor: r-devel-linux-x86_64-debian-gcc