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### Running command:
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###   /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
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Macarron.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* 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 ...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 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   72.521  0.805  73.367
decorateID  0.151  0.015  34.681
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Macarron.Rcheck/00check.log’
for details.