############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Macarron.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Macarron_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Macarron.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 252.909 1.543 254.463 showBest 9.691 0.392 10.083 prioritize 9.027 0.386 9.413 calES 7.702 0.167 7.869 calQval 7.585 0.091 7.676 calAVA 5.240 0.049 5.288 decorateID 1.081 0.043 13.076 * 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: 2025-02-04 00:04:58.257356 WARNING::Deleting existing fitted file: maaslin2_output/fits/fitted.rds 2025-02-04 00:04:58.25936 INFO::Writing fitted values to file maaslin2_output/fits/fitted.rds 2025-02-04 00:04:58.295553 INFO::Writing all results to file (ordered by increasing q-values): maaslin2_output/all_results.tsv 2025-02-04 00:04:58.31088 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/Macarron.Rcheck/00check.log’ for details.