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This page was generated on 2026-04-30 11:36 -0400 (Thu, 30 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4988
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-04-24 r89963) -- "Because it was There" 4718
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

Package 1199/2418HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.26.0  (landing page)
Sagun Maharjan
Snapshot Date: 2026-04-29 13:40 -0400 (Wed, 29 Apr 2026)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_23
git_last_commit: 0616fc9
git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
See other builds for Maaslin2 in R Universe.

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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2026-04-29 20:32:26 -0400 (Wed, 29 Apr 2026)
EndedAt: 2026-04-29 20:33:37 -0400 (Wed, 29 Apr 2026)
EllapsedTime: 70.8 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-30 00:32:26 UTC
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.26.0’
* 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 39.929  0.513  40.574
* 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/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.26.0’
** 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 version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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"
2026-04-29 20:33:22.876762 INFO::Writing function arguments to log file
2026-04-29 20:33:22.888307 INFO::Verifying options selected are valid
2026-04-29 20:33:22.902291 INFO::Determining format of input files
2026-04-29 20:33:22.903149 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-29 20:33:22.905722 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-29 20:33:22.906304 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-29 20:33:22.910429 INFO::Filter data based on min abundance and min prevalence
2026-04-29 20:33:22.911009 INFO::Total samples in data: 1595
2026-04-29 20:33:22.911437 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-29 20:33:22.913348 INFO::Total filtered features: 0
2026-04-29 20:33:22.9142 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-29 20:33:22.917594 INFO::Total filtered features with variance filtering: 0
2026-04-29 20:33:22.918205 INFO::Filtered feature names from variance filtering:
2026-04-29 20:33:22.918651 INFO::Running selected normalization method: TSS
2026-04-29 20:33:23.329938 INFO::Bypass z-score application to metadata
2026-04-29 20:33:23.330624 INFO::Running selected transform method: AST
2026-04-29 20:33:23.34009 INFO::Running selected analysis method: LM
2026-04-29 20:33:23.584021 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-29 20:33:23.813414 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-29 20:33:23.876752 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-29 20:33:23.930703 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-29 20:33:23.993013 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-29 20:33:24.050047 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-29 20:33:24.100773 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-29 20:33:24.157162 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-29 20:33:24.212499 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-29 20:33:24.261513 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-29 20:33:24.311637 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-29 20:33:24.382773 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-29 20:33:24.432052 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-29 20:33:24.484471 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-29 20:33:24.537897 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-29 20:33:24.596699 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-29 20:33:24.646788 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-29 20:33:24.702508 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-29 20:33:24.759083 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-29 20:33:24.806964 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-29 20:33:24.861241 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-29 20:33:24.918519 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-29 20:33:24.971767 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-29 20:33:25.022209 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-29 20:33:25.079821 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-29 20:33:25.132615 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-29 20:33:25.183377 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-29 20:33:25.243879 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-29 20:33:25.295617 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-29 20:33:25.348512 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-29 20:33:25.402015 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-29 20:33:25.455179 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-29 20:33:25.505055 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-29 20:33:25.563819 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-29 20:33:25.613699 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-29 20:33:25.675611 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-29 20:33:25.731044 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-29 20:33:25.786591 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-29 20:33:25.842525 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-29 20:33:25.892318 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-29 20:33:25.951708 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-29 20:33:26.002289 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-29 20:33:26.054508 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-29 20:33:26.109392 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-29 20:33:26.159278 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-29 20:33:26.210043 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-29 20:33:26.265914 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-29 20:33:26.32151 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-29 20:33:26.373212 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-29 20:33:26.428229 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-29 20:33:26.477954 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-29 20:33:26.528744 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-29 20:33:26.586577 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-29 20:33:26.642503 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-29 20:33:26.695483 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-29 20:33:26.752769 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-29 20:33:26.810289 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-29 20:33:26.866157 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-29 20:33:26.919414 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-29 20:33:26.970566 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-29 20:33:27.026989 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-29 20:33:27.081507 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-29 20:33:27.137842 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-29 20:33:27.189654 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-29 20:33:27.243257 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-29 20:33:27.302028 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-29 20:33:27.355982 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-29 20:33:27.408529 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-29 20:33:27.462128 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-29 20:33:27.523274 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-29 20:33:27.592757 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-29 20:33:27.749896 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-29 20:33:27.800427 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-29 20:33:27.849205 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-29 20:33:27.899747 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-29 20:33:27.95261 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-29 20:33:28.002824 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-29 20:33:28.056088 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-29 20:33:28.117388 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-29 20:33:28.172631 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-29 20:33:28.223589 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-29 20:33:28.278447 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-29 20:33:28.333921 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-29 20:33:28.383949 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-29 20:33:28.437421 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-29 20:33:28.491064 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-29 20:33:28.542393 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-29 20:33:28.610145 INFO::Counting total values for each feature
2026-04-29 20:33:28.622145 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-29 20:33:28.669958 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-29 20:33:28.72612 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-29 20:33:28.783087 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-29 20:33:28.809949 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-29 20:33:28.823941 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-29 20:33:28.827389 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-29 20:33:28.834705 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"
2026-04-29 20:33:28.84112 INFO::Writing function arguments to log file
2026-04-29 20:33:28.84452 INFO::Verifying options selected are valid
2026-04-29 20:33:28.844963 INFO::Determining format of input files
2026-04-29 20:33:28.845497 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-29 20:33:28.847771 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-29 20:33:28.848217 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-04-29 20:33:28.848892 INFO::Filter data based on min abundance and min prevalence
2026-04-29 20:33:28.84926 INFO::Total samples in data: 1595
2026-04-29 20:33:28.84961 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-29 20:33:28.851053 INFO::Total filtered features: 0
2026-04-29 20:33:28.85145 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-29 20:33:28.854207 INFO::Total filtered features with variance filtering: 0
2026-04-29 20:33:28.854861 INFO::Filtered feature names from variance filtering:
2026-04-29 20:33:28.855314 INFO::Running selected normalization method: NONE
2026-04-29 20:33:28.855687 INFO::Bypass z-score application to metadata
2026-04-29 20:33:28.856059 INFO::Running selected transform method: AST
2026-04-29 20:33:28.861621 INFO::Running selected analysis method: LM
2026-04-29 20:33:28.862359 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-29 20:33:28.91327 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-29 20:33:28.966441 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-29 20:33:29.018504 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-29 20:33:29.069735 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-29 20:33:29.122826 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-29 20:33:29.178411 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-29 20:33:29.230132 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-29 20:33:29.278762 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-29 20:33:29.330333 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-29 20:33:29.386421 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-29 20:33:29.436852 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-29 20:33:29.487826 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-29 20:33:29.541219 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-29 20:33:29.59637 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-29 20:33:29.649056 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-29 20:33:29.699121 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-29 20:33:29.757357 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-29 20:33:29.806422 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-29 20:33:29.85201 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-29 20:33:29.900959 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-29 20:33:29.954506 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-29 20:33:30.005401 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-29 20:33:30.055241 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-29 20:33:30.111429 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-29 20:33:30.165563 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-29 20:33:30.2189 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-29 20:33:30.27043 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-29 20:33:30.321722 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-29 20:33:30.36794 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-29 20:33:30.417933 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-29 20:33:30.467393 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-29 20:33:30.521038 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-29 20:33:30.567807 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-29 20:33:30.617619 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-29 20:33:30.668437 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-29 20:33:30.718342 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-29 20:33:30.770919 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-29 20:33:30.823848 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-29 20:33:30.869136 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-29 20:33:30.915702 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-29 20:33:30.967244 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-29 20:33:31.015907 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-29 20:33:31.067653 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-29 20:33:31.124933 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-29 20:33:31.17755 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-29 20:33:31.229435 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-29 20:33:31.281468 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-29 20:33:31.33097 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-29 20:33:31.382195 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-29 20:33:31.426023 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-29 20:33:31.475111 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-29 20:33:31.534123 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-29 20:33:31.577707 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-29 20:33:31.625028 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-29 20:33:31.674564 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-29 20:33:31.729993 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-29 20:33:31.779778 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-29 20:33:31.828792 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-29 20:33:31.883192 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-29 20:33:31.932616 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-29 20:33:31.984595 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-29 20:33:32.036229 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-29 20:33:32.094241 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-29 20:33:32.142646 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-29 20:33:32.191704 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-29 20:33:32.242178 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-29 20:33:32.297623 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-29 20:33:32.346427 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-29 20:33:32.399902 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-29 20:33:32.454923 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-29 20:33:32.510741 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-29 20:33:32.52907 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-29 20:33:32.582086 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-29 20:33:32.632757 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-29 20:33:32.69042 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-29 20:33:32.742432 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-29 20:33:32.797295 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-29 20:33:32.847943 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-29 20:33:32.904045 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-29 20:33:32.954358 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-29 20:33:33.002003 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-29 20:33:33.058308 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-29 20:33:33.105931 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-29 20:33:33.154399 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-29 20:33:33.202616 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-29 20:33:33.255541 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-29 20:33:33.307125 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-29 20:33:33.367932 INFO::Counting total values for each feature
2026-04-29 20:33:33.381862 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-29 20:33:33.428686 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-29 20:33:33.475358 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-29 20:33:33.529906 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-29 20:33:33.565034 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-29 20:33:33.598814 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-29 20:33:33.602205 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-29 20:33:33.604801 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 
 10.963   0.201  11.190

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin239.929 0.51340.574