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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings microbiomeMarker_1.12.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/microbiomeMarker.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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    19.035  0.296  19.386
plot_cladogram 12.456  0.200  12.684
run_aldex      11.343  0.578  11.959
run_lefse       8.140  0.136   8.299
plot_heatmap    8.042  0.056   8.116
run_deseq2      7.672  0.158   7.852
plot_abundance  6.272  0.059   6.346
plot_sl_roc     5.804  0.305   6.338
* 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

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL microbiomeMarker
###
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* installing to library ‘/home/biocbuild/R/R-4.4.3/site-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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 0 | WARN 6 | 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:22:5'
• empty test (1): 'test-ancombc.R:1:1'

[ FAIL 0 | WARN 6 | SKIP 8 | PASS 220 ]
> 
> proc.time()
   user  system elapsed 
 93.538   3.291  97.539