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###
### Running command:
###
###   /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_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.11.0’
* 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 ‘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              49.866  0.391  57.076
run_aldex                21.709  1.544  26.739
plot_cladogram           21.060  0.317  23.007
plot_heatmap             16.300  0.519  19.119
run_deseq2               14.491  0.102  16.717
run_lefse                13.534  0.129  17.209
plot_abundance           11.060  0.067  12.455
plot_sl_roc              10.192  0.265  11.803
run_metagenomeseq         9.409  0.093  11.222
effect_size-plot          9.132  0.085   9.973
run_test_multiple_groups  8.570  0.064   9.781
run_test_two_groups       8.545  0.049  10.019
run_simple_stat           7.911  0.053   9.072
assign-marker_table       7.581  0.242   8.277
run_limma_voom            7.756  0.050   9.196
subset_marker             7.667  0.044   8.688
run_edger                 7.390  0.060   9.104
marker_table-methods      7.322  0.043   8.087
run_sl                    4.345  0.055   5.096
* 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-3.20-bioc/meat/microbiomeMarker.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microbiomeMarker
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘microbiomeMarker’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (microbiomeMarker)

R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(microbiomeMarker)
> 
> test_check("microbiomeMarker")
conditions vector supplied
operating in serial mode
computing center with all features
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
operating in serial mode
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
Default value being used.
Default value being used.
Default value being used.
Default value being used.
converting counts to integer mode
Loading required package: ggplot2
Loading required package: lattice
[ FAIL 1 | WARN 42 | SKIP 8 | PASS 220 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• 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