############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Macarron.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Macarron_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Macarron.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (conda-forge gcc 14.2.0-1) 14.2.0 GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Macarron/DESCRIPTION’ ... OK * this is package ‘Macarron’ version ‘1.11.0’ * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Macarron’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘stringr’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calQval: no visible binding for global variable ‘metadata’ calQval: no visible binding for global variable ‘value’ calQval: no visible binding for global variable ‘pval’ Undefined global functions or variables: metadata pval value * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'Macarron.Rd': Macarron Code: function(input_abundances, input_annotations, input_metadata, input_taxonomy, output = "Macarron_output", metadata_variable = 1, min_prevalence = 0.7, execution_mode = "serial", standard_identifier = 1, anchor_annotation = 2, min_module_size = NULL, fixed_effects = NULL, random_effects = NULL, reference = NULL, cores = 1, plot_heatmap = FALSE, plot_scatter = TRUE, heatmap_first_n = 50, show_best = TRUE, priority_threshold = 0.9, per_module = 10, per_phenotype = 1000, only_characterizable = TRUE) Docs: function(input_abundances, input_annotations, input_metadata, input_taxonomy, output = "Macarron_output", metadata_variable = 1, min_prevalence = 0.7, execution_mode = "serial", standard_identifier = 1, anchor_annotation = 2, min_module_size = NULL, fixed_effects = NULL, random_effects = NULL, reference = NULL, cores = 1, plot_heatmap = TRUE, plot_scatter = FALSE, heatmap_first_n = 50, show_best = TRUE, priority_threshold = 0.9, per_module = 10, per_phenotype = 1000, only_characterizable = TRUE) Mismatches in argument default values: Name: 'plot_heatmap' Code: FALSE Docs: TRUE Name: 'plot_scatter' Code: TRUE Docs: FALSE Codoc mismatches from Rd file 'calQval.Rd': calQval Code: function(se, mod.assn, metadata_variable = 1, fixed_effects = NULL, random_effects = NULL, reference = NULL, output_folder = NULL, cores = 1, plot_heatmap = FALSE, plot_scatter = FALSE, heatmap_first_n = 50) Docs: function(se, mod.assn, metadata_variable = 1, fixed_effects = NULL, random_effects = NULL, reference = NULL, output_folder = NULL, cores = 1, plot_heatmap = TRUE, plot_scatter = FALSE, heatmap_first_n = 50) Mismatches in argument default values: Name: 'plot_heatmap' Code: FALSE Docs: TRUE * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Macarron 369.731 2.682 373.326 showBest 16.927 0.663 17.452 prioritize 16.269 0.299 16.432 calQval 13.805 0.148 13.811 calES 13.662 0.103 13.627 calAVA 10.746 0.100 10.695 findMacMod 6.686 0.120 6.644 makeDisMat 5.312 0.068 5.260 decorateID 0.388 0.052 63.409 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/Macarron.Rcheck/00check.log’ for details.