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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeMarker_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.12.2’
* 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 ‘microbiomeMarker’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
run_ancombc              33.620  0.127  34.456
run_aldex                21.571  1.374  23.572
plot_cladogram           20.160  0.276  22.143
plot_heatmap             15.504  0.177  17.031
run_lefse                13.733  0.156  14.156
run_deseq2               12.990  0.079  13.212
plot_abundance           10.210  0.041  10.500
plot_sl_roc               9.877  0.182  11.375
run_metagenomeseq         8.231  0.080   8.362
run_test_multiple_groups  7.705  0.023   7.802
run_test_two_groups       7.631  0.025   7.704
assign-marker_table       7.200  0.309   7.817
effect_size-plot          7.042  0.059   7.296
run_edger                 6.974  0.027   7.130
run_limma_voom            6.936  0.064   7.400
run_simple_stat           6.949  0.035   7.012
marker_table-methods      6.773  0.029   7.049
subset_marker             6.648  0.020   6.679
* 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: OK