Multiple platform build/check report for BioC 3.23 - CHECK results for Maaslin2 on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4891
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4583
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for Maaslin2 on kjohnson3

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: Maaslin2

Version: 1.25.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.25.1.tar.gz

StartedAt: 2026-03-04 20:36:44 -0500 (Wed, 04 Mar 2026)

EndedAt: 2026-03-04 20:38:03 -0500 (Wed, 04 Mar 2026)

EllapsedTime: 79.1 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.25.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘Maaslin2’ 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 ... NOTE
Maaslin2: no visible binding for global variable ‘var’
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  var xnames
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 42.346  0.688  45.377
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.25.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-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(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2026-03-04 20:37:47.231116 INFO::Writing function arguments to log file
2026-03-04 20:37:47.249811 INFO::Verifying options selected are valid
2026-03-04 20:37:47.264507 INFO::Determining format of input files
2026-03-04 20:37:47.265218 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 20:37:47.267684 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-04 20:37:47.268199 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-03-04 20:37:47.269099 INFO::Filter data based on min abundance and min prevalence
2026-03-04 20:37:47.269411 INFO::Total samples in data: 1595
2026-03-04 20:37:47.269694 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-04 20:37:47.271323 INFO::Total filtered features: 0
2026-03-04 20:37:47.271713 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-04 20:37:47.274628 INFO::Total filtered features with variance filtering: 0
2026-03-04 20:37:47.275066 INFO::Filtered feature names from variance filtering:
2026-03-04 20:37:47.27538 INFO::Running selected normalization method: TSS
2026-03-04 20:37:47.738512 INFO::Bypass z-score application to metadata
2026-03-04 20:37:47.739014 INFO::Running selected transform method: AST
2026-03-04 20:37:47.744762 INFO::Running selected analysis method: LM
2026-03-04 20:37:48.015762 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-04 20:37:48.280658 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-04 20:37:48.350495 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-04 20:37:48.412636 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-04 20:37:48.473517 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-04 20:37:48.544672 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-04 20:37:48.6067 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-04 20:37:48.668607 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-04 20:37:48.744017 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-04 20:37:48.79652 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-04 20:37:48.863619 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-04 20:37:48.939463 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-04 20:37:48.996141 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-04 20:37:49.050796 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-04 20:37:49.12209 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-04 20:37:49.182858 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-04 20:37:49.236323 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-04 20:37:49.303583 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-04 20:37:49.359246 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-04 20:37:49.419357 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-04 20:37:49.478442 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-04 20:37:49.534319 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-04 20:37:49.590505 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-04 20:37:49.659109 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-04 20:37:49.721118 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-04 20:37:49.779738 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-04 20:37:49.841375 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-04 20:37:49.899348 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-04 20:37:49.964334 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-04 20:37:50.038282 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-04 20:37:50.098346 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-04 20:37:50.159908 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-04 20:37:50.215357 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-04 20:37:50.271158 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-04 20:37:50.334367 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-04 20:37:50.392131 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-04 20:37:50.457304 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-04 20:37:50.521244 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-04 20:37:50.579578 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-04 20:37:50.636423 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-04 20:37:50.696293 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-04 20:37:50.764211 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-04 20:37:50.82516 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-04 20:37:50.886058 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-04 20:37:50.957448 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-04 20:37:51.022391 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-04 20:37:51.233646 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-04 20:37:51.295868 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-04 20:37:51.356311 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-04 20:37:51.421047 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-04 20:37:51.490344 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-04 20:37:51.546827 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-04 20:37:51.615001 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-04 20:37:51.680274 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-04 20:37:51.731382 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-04 20:37:51.795306 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-04 20:37:51.85591 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-04 20:37:51.913159 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-04 20:37:51.967318 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-04 20:37:52.017927 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-04 20:37:52.072746 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-04 20:37:52.130819 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-04 20:37:52.182684 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-04 20:37:52.238828 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-04 20:37:52.296254 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-04 20:37:52.357397 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-04 20:37:52.409714 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-04 20:37:52.464092 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-04 20:37:52.530738 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-04 20:37:52.597052 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-04 20:37:52.659445 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-04 20:37:52.724019 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-04 20:37:52.783401 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-04 20:37:52.841133 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-04 20:37:52.894929 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-04 20:37:52.958912 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-04 20:37:53.027828 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-04 20:37:53.083129 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-04 20:37:53.146931 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-04 20:37:53.209701 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-04 20:37:53.26688 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-04 20:37:53.326044 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-04 20:37:53.38428 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-04 20:37:53.442526 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-04 20:37:53.509982 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-04 20:37:53.571979 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-04 20:37:53.631628 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-04 20:37:53.716446 INFO::Counting total values for each feature
2026-03-04 20:37:53.730391 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-03-04 20:37:53.779624 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-03-04 20:37:53.842862 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-03-04 20:37:53.90156 INFO::Writing residuals to file output/fits/residuals.rds
2026-03-04 20:37:53.938631 INFO::Writing fitted values to file output/fits/fitted.rds
2026-03-04 20:37:53.953321 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-03-04 20:37:53.956293 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-03-04 20:37:53.959238 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2026-03-04 20:37:53.965717 INFO::Writing function arguments to log file
2026-03-04 20:37:53.968029 INFO::Verifying options selected are valid
2026-03-04 20:37:53.968371 INFO::Determining format of input files
2026-03-04 20:37:53.968779 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 20:37:53.970745 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-04 20:37:53.971088 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-03-04 20:37:53.971643 INFO::Filter data based on min abundance and min prevalence
2026-03-04 20:37:53.971919 INFO::Total samples in data: 1595
2026-03-04 20:37:53.972184 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-04 20:37:53.973579 INFO::Total filtered features: 0
2026-03-04 20:37:53.973888 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-04 20:37:53.976457 INFO::Total filtered features with variance filtering: 0
2026-03-04 20:37:53.976784 INFO::Filtered feature names from variance filtering:
2026-03-04 20:37:53.97705 INFO::Running selected normalization method: NONE
2026-03-04 20:37:53.977308 INFO::Bypass z-score application to metadata
2026-03-04 20:37:53.977572 INFO::Running selected transform method: AST
2026-03-04 20:37:53.982969 INFO::Running selected analysis method: LM
2026-03-04 20:37:53.983478 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-04 20:37:54.166913 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-04 20:37:54.21964 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-04 20:37:54.283993 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-04 20:37:54.348111 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-04 20:37:54.427591 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-04 20:37:54.495179 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-04 20:37:54.561176 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-04 20:37:54.623663 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-04 20:37:54.681609 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-04 20:37:54.740758 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-04 20:37:54.815347 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-04 20:37:54.878323 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-04 20:37:54.930524 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-04 20:37:54.986096 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-04 20:37:55.044894 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-04 20:37:55.099882 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-04 20:37:55.155766 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-04 20:37:55.209515 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-04 20:37:55.275008 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-04 20:37:55.344054 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-04 20:37:55.415146 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-04 20:37:55.470235 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-04 20:37:55.525122 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-04 20:37:55.58513 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-04 20:37:55.649527 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-04 20:37:55.703436 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-04 20:37:55.774233 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-04 20:37:55.832663 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-04 20:37:55.881962 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-04 20:37:55.933311 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-04 20:37:55.994795 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-04 20:37:56.053075 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-04 20:37:56.109639 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-04 20:37:56.162804 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-04 20:37:56.219465 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-04 20:37:56.275427 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-04 20:37:56.336856 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-04 20:37:56.392954 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-04 20:37:56.445398 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-04 20:37:56.500028 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-04 20:37:56.560935 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-04 20:37:56.615118 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-04 20:37:56.678805 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-04 20:37:56.745986 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-04 20:37:56.821095 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-04 20:37:56.889782 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-04 20:37:56.944176 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-04 20:37:57.002421 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-04 20:37:57.062439 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-04 20:37:57.112156 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-04 20:37:57.175277 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-04 20:37:57.232295 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-04 20:37:57.282745 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-04 20:37:57.331438 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-04 20:37:57.396059 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-04 20:37:57.457483 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-04 20:37:57.516194 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-04 20:37:57.5696 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-04 20:37:57.628918 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-04 20:37:57.679143 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-04 20:37:57.740227 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-04 20:37:57.802528 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-04 20:37:57.875268 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-04 20:37:57.936899 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-04 20:37:57.99623 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-04 20:37:58.048977 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-04 20:37:58.106734 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-04 20:37:58.159329 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-04 20:37:58.217173 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-04 20:37:58.279418 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-04 20:37:58.339237 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-04 20:37:58.367525 WARNING::Fitting problem for feature 72 a warning was issued
2026-03-04 20:37:58.424197 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-04 20:37:58.481682 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-04 20:37:58.538638 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-04 20:37:58.595355 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-04 20:37:58.649723 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-04 20:37:58.704603 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-04 20:37:58.768075 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-04 20:37:58.821922 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-04 20:37:58.875796 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-04 20:37:58.93569 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-04 20:37:59.002066 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-04 20:37:59.055092 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-04 20:37:59.115278 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-04 20:37:59.168425 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-04 20:37:59.231717 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-04 20:37:59.296139 INFO::Counting total values for each feature
2026-03-04 20:37:59.307814 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-03-04 20:37:59.366905 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-03-04 20:37:59.419266 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-03-04 20:37:59.487983 INFO::Writing residuals to file output2/fits/residuals.rds
2026-03-04 20:37:59.526034 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-03-04 20:37:59.574103 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-03-04 20:37:59.578787 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-03-04 20:37:59.581278 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 11.881   0.312  12.927

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	42.346	0.688	45.377