############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Macarron.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Macarron_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Macarron.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Macarron/DESCRIPTION’ ... OK * this is package ‘Macarron’ version ‘1.10.0’ * 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 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 588.706 5.365 630.161 prioritize 22.313 0.522 24.324 showBest 21.658 0.532 23.117 calQval 16.004 0.532 17.696 calES 15.842 0.549 16.867 calAVA 10.738 0.136 11.449 findMacMod 4.899 0.071 5.010 decorateID 0.591 0.059 120.500 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 2024-12-20 05:56:22.980261 WARNING::Deleting existing fitted file: maaslin2_output/fits/fitted.rds 2024-12-20 05:56:22.984476 INFO::Writing fitted values to file maaslin2_output/fits/fitted.rds 2024-12-20 05:56:23.052765 INFO::Writing all results to file (ordered by increasing q-values): maaslin2_output/all_results.tsv 2024-12-20 05:56:23.099525 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): maaslin2_output/significant_results.tsv [ FAIL 1 | WARN 103 | SKIP 0 | PASS 19 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-decorateID.R:12:1'): (code run outside of `test_that()`) ───── dim(decorate_output) not equal to dim(taxonomy_df). 1/2 mismatches [1] 6 - 7 == -1 [ FAIL 1 | WARN 103 | SKIP 0 | PASS 19 ] Error: Test failures Execution halted * 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: 1 ERROR, 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Macarron.Rcheck/00check.log’ for details.