• using R Under development (unstable) (2025-09-01 r88761)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-1) 15.2.0     GNU Fortran (Debian 15.2.0-1) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘OmicFlow/DESCRIPTION’ ... OK
• this is package ‘OmicFlow’ version ‘1.3.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] OK
• 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 the install log 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 ... [3s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [3s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/3s] 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 ... [14s/18s] OK
• checking Rd files ... [0s/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 ... [8s/8s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [14s/16s] 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
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR