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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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ 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 ‘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              51.508  0.644  61.242
run_aldex                22.143  1.508  27.754
plot_cladogram           22.888  0.312  27.305
plot_heatmap             15.216  0.303  21.386
run_deseq2               14.804  0.146  17.200
run_lefse                13.917  0.187  17.017
plot_abundance           12.582  0.096  14.313
plot_sl_roc              10.577  0.236  12.700
run_metagenomeseq         9.375  0.102  11.693
run_test_two_groups       8.942  0.192  10.536
run_test_multiple_groups  8.793  0.057  10.183
effect_size-plot          8.233  0.092   9.826
assign-marker_table       8.030  0.254   9.598
run_limma_voom            7.977  0.048  10.123
run_simple_stat           7.963  0.044   8.935
marker_table-methods      7.738  0.078   9.728
subset_marker             7.669  0.048   8.695
run_edger                 7.598  0.065   9.147
* 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:
  • On CRAN (7): 'test-ancom.R:46:5', 'test-edgeR.R:9:5', 'test-lefse.R:19:5',
    'test-limma-voom.R:15:5', 'test-multiple-groups-test.R:27:5',
    'test-multiple-groups-test.R:54:9', 'test-two-group-test.R:24:5'
  • empty test (1): 'test-ancombc.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-confounder.R:42:5'): confounder analysis ─────────────────────
  res$pvalue (`actual`) not equal to 0.239 (`expected`).
  
    `actual`: 0.4
  `expected`: 0.2
  
  [ FAIL 1 | WARN 42 | SKIP 8 | PASS 220 ]
  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
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/microbiomeMarker.Rcheck/00check.log’
for details.