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"	4877
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4570
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: 2026-02-27 20:51:02 -0500 (Fri, 27 Feb 2026)

EndedAt: 2026-02-27 20:52:22 -0500 (Fri, 27 Feb 2026)

EllapsedTime: 80.1 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 42.485  0.698  45.488
* 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"
2026-02-27 20:52:05.560379 INFO::Writing function arguments to log file
2026-02-27 20:52:05.57728 INFO::Verifying options selected are valid
2026-02-27 20:52:05.590604 INFO::Determining format of input files
2026-02-27 20:52:05.591233 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-27 20:52:05.5934 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-02-27 20:52:05.59387 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-02-27 20:52:05.595646 INFO::Filter data based on min abundance and min prevalence
2026-02-27 20:52:05.596793 INFO::Total samples in data: 1595
2026-02-27 20:52:05.597623 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-02-27 20:52:05.601377 INFO::Total filtered features: 0
2026-02-27 20:52:05.602622 INFO::Filtered feature names from abundance and prevalence filtering:
2026-02-27 20:52:05.609554 INFO::Total filtered features with variance filtering: 0
2026-02-27 20:52:05.61079 INFO::Filtered feature names from variance filtering:
2026-02-27 20:52:05.611658 INFO::Running selected normalization method: TSS
2026-02-27 20:52:06.072269 INFO::Bypass z-score application to metadata
2026-02-27 20:52:06.072757 INFO::Running selected transform method: AST
2026-02-27 20:52:06.078724 INFO::Running selected analysis method: LM
2026-02-27 20:52:06.380867 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-02-27 20:52:06.648083 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-02-27 20:52:06.722969 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-02-27 20:52:06.778637 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-02-27 20:52:06.835832 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-02-27 20:52:06.905237 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-02-27 20:52:06.959701 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-02-27 20:52:07.051906 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-02-27 20:52:07.128879 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-02-27 20:52:07.183383 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-02-27 20:52:07.243181 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-02-27 20:52:07.32707 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-02-27 20:52:07.392715 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-02-27 20:52:07.460729 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-02-27 20:52:07.529701 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-02-27 20:52:07.589921 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-02-27 20:52:07.644847 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-02-27 20:52:07.719934 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-02-27 20:52:07.775517 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-02-27 20:52:07.828224 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-02-27 20:52:07.888349 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-02-27 20:52:07.948069 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-02-27 20:52:08.005944 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-02-27 20:52:08.072687 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-02-27 20:52:08.132817 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-02-27 20:52:08.198085 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-02-27 20:52:08.260816 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-02-27 20:52:08.327542 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-02-27 20:52:08.395886 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-02-27 20:52:08.464347 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-02-27 20:52:08.523051 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-02-27 20:52:08.597754 INFO::Fitting model to feature number 32, Prevotella.copri
2026-02-27 20:52:08.653651 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-02-27 20:52:08.722092 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-02-27 20:52:08.779591 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-02-27 20:52:08.842046 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-02-27 20:52:08.910543 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-02-27 20:52:08.987926 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-02-27 20:52:09.04206 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-02-27 20:52:09.105869 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-02-27 20:52:09.16702 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-02-27 20:52:09.220751 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-02-27 20:52:09.305044 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-02-27 20:52:09.360069 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-02-27 20:52:09.423395 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-02-27 20:52:09.487332 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-02-27 20:52:09.568745 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-02-27 20:52:09.631523 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-02-27 20:52:09.695594 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-02-27 20:52:09.766283 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-02-27 20:52:09.833753 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-02-27 20:52:09.889148 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-02-27 20:52:09.947386 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-02-27 20:52:10.015284 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-02-27 20:52:10.065494 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-02-27 20:52:10.134167 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-02-27 20:52:10.197843 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-02-27 20:52:10.26436 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-02-27 20:52:10.331606 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-02-27 20:52:10.386796 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-02-27 20:52:10.454924 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-02-27 20:52:10.510855 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-02-27 20:52:10.577978 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-02-27 20:52:10.64626 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-02-27 20:52:10.715949 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-02-27 20:52:10.778222 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-02-27 20:52:10.832629 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-02-27 20:52:10.887718 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-02-27 20:52:11.081515 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-02-27 20:52:11.149822 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-02-27 20:52:11.217442 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-02-27 20:52:11.280425 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-02-27 20:52:11.33765 INFO::Fitting model to feature number 73, Dialister.invisus
2026-02-27 20:52:11.398967 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-02-27 20:52:11.45336 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-02-27 20:52:11.517881 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-02-27 20:52:11.571991 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-02-27 20:52:11.636119 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-02-27 20:52:11.695267 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-02-27 20:52:11.774377 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-02-27 20:52:11.83649 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-02-27 20:52:11.899166 INFO::Fitting model to feature number 82, Escherichia.coli
2026-02-27 20:52:11.964975 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-02-27 20:52:12.02424 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-02-27 20:52:12.094354 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-02-27 20:52:12.153084 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-02-27 20:52:12.213926 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-02-27 20:52:12.287862 INFO::Counting total values for each feature
2026-02-27 20:52:12.299686 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-02-27 20:52:12.353858 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-02-27 20:52:12.417167 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-02-27 20:52:12.482442 INFO::Writing residuals to file output/fits/residuals.rds
2026-02-27 20:52:12.509919 INFO::Writing fitted values to file output/fits/fitted.rds
2026-02-27 20:52:12.525424 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-02-27 20:52:12.528596 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-02-27 20:52:12.531505 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"
2026-02-27 20:52:12.53856 INFO::Writing function arguments to log file
2026-02-27 20:52:12.54074 INFO::Verifying options selected are valid
2026-02-27 20:52:12.541079 INFO::Determining format of input files
2026-02-27 20:52:12.541518 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-27 20:52:12.543556 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-02-27 20:52:12.543923 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-02-27 20:52:12.544506 INFO::Filter data based on min abundance and min prevalence
2026-02-27 20:52:12.544794 INFO::Total samples in data: 1595
2026-02-27 20:52:12.54546 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-02-27 20:52:12.549413 INFO::Total filtered features: 0
2026-02-27 20:52:12.550858 INFO::Filtered feature names from abundance and prevalence filtering:
2026-02-27 20:52:12.558277 INFO::Total filtered features with variance filtering: 0
2026-02-27 20:52:12.559924 INFO::Filtered feature names from variance filtering:
2026-02-27 20:52:12.560908 INFO::Running selected normalization method: NONE
2026-02-27 20:52:12.561396 INFO::Bypass z-score application to metadata
2026-02-27 20:52:12.561706 INFO::Running selected transform method: AST
2026-02-27 20:52:12.5749 INFO::Running selected analysis method: LM
2026-02-27 20:52:12.575734 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-02-27 20:52:12.630584 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-02-27 20:52:12.695503 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-02-27 20:52:12.750238 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-02-27 20:52:12.805468 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-02-27 20:52:12.858863 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-02-27 20:52:12.914605 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-02-27 20:52:12.977524 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-02-27 20:52:13.028797 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-02-27 20:52:13.087173 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-02-27 20:52:13.141351 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-02-27 20:52:13.207207 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-02-27 20:52:13.260179 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-02-27 20:52:13.320507 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-02-27 20:52:13.394125 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-02-27 20:52:13.448856 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-02-27 20:52:13.508469 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-02-27 20:52:13.567117 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-02-27 20:52:13.629411 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-02-27 20:52:13.69257 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-02-27 20:52:13.74571 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-02-27 20:52:13.807826 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-02-27 20:52:13.883526 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-02-27 20:52:13.9353 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-02-27 20:52:14.000755 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-02-27 20:52:14.054056 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-02-27 20:52:14.110309 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-02-27 20:52:14.164843 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-02-27 20:52:14.225358 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-02-27 20:52:14.279733 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-02-27 20:52:14.336617 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-02-27 20:52:14.388743 INFO::Fitting model to feature number 32, Prevotella.copri
2026-02-27 20:52:14.44777 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-02-27 20:52:14.505843 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-02-27 20:52:14.558902 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-02-27 20:52:14.612998 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-02-27 20:52:14.672183 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-02-27 20:52:14.733831 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-02-27 20:52:14.791388 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-02-27 20:52:14.840334 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-02-27 20:52:14.894729 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-02-27 20:52:14.95204 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-02-27 20:52:15.0103 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-02-27 20:52:15.068122 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-02-27 20:52:15.131347 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-02-27 20:52:15.190871 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-02-27 20:52:15.247884 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-02-27 20:52:15.323156 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-02-27 20:52:15.386711 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-02-27 20:52:15.445539 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-02-27 20:52:15.494748 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-02-27 20:52:15.546307 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-02-27 20:52:15.604331 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-02-27 20:52:15.650694 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-02-27 20:52:15.709688 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-02-27 20:52:15.762824 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-02-27 20:52:15.823767 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-02-27 20:52:15.881823 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-02-27 20:52:15.932361 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-02-27 20:52:15.997296 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-02-27 20:52:16.045406 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-02-27 20:52:16.102503 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-02-27 20:52:16.150981 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-02-27 20:52:16.212463 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-02-27 20:52:16.26206 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-02-27 20:52:16.314037 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-02-27 20:52:16.364543 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-02-27 20:52:16.420988 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-02-27 20:52:16.471183 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-02-27 20:52:16.529402 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-02-27 20:52:16.589436 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-02-27 20:52:16.65467 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-02-27 20:52:16.67307 WARNING::Fitting problem for feature 72 a warning was issued
2026-02-27 20:52:16.736141 INFO::Fitting model to feature number 73, Dialister.invisus
2026-02-27 20:52:16.787784 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-02-27 20:52:16.854327 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-02-27 20:52:16.905977 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-02-27 20:52:16.958009 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-02-27 20:52:17.015322 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-02-27 20:52:17.072622 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-02-27 20:52:17.126742 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-02-27 20:52:17.177014 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-02-27 20:52:17.242621 INFO::Fitting model to feature number 82, Escherichia.coli
2026-02-27 20:52:17.30265 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-02-27 20:52:17.353103 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-02-27 20:52:17.411595 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-02-27 20:52:17.470092 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-02-27 20:52:17.530033 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-02-27 20:52:17.596154 INFO::Counting total values for each feature
2026-02-27 20:52:17.607712 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-02-27 20:52:17.658914 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-02-27 20:52:17.710609 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-02-27 20:52:17.78201 INFO::Writing residuals to file output2/fits/residuals.rds
2026-02-27 20:52:17.823853 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-02-27 20:52:17.861652 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-02-27 20:52:17.865132 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-02-27 20:52:17.867631 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 
 11.848   0.333  12.885

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	42.485	0.698	45.488