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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Macarron.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Macarron_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Macarron.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Macarron/DESCRIPTION’ ... OK
* this is package ‘Macarron’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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   223.058  0.718 223.790
prioritize   8.901  0.402   9.304
showBest     8.887  0.330   9.217
calQval      6.345  0.039   6.385
calES        6.315  0.049   6.366
calAVA       5.753  0.029   5.781
decorateID   1.066  0.057 298.982
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Macarron.Rcheck/00check.log’
for details.