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This page was generated on 2025-09-11 12:05 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1149/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 43d70cc
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on lconway

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: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2025-09-10 22:53:04 -0400 (Wed, 10 Sep 2025)
EndedAt: 2025-09-10 22:56:08 -0400 (Wed, 10 Sep 2025)
EllapsedTime: 183.9 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.23.0’
* 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_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* 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 98.974  1.772 101.494
* 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-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.23.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-09-10 22:55:26.366941 INFO::Writing function arguments to log file
2025-09-10 22:55:26.426989 INFO::Verifying options selected are valid
2025-09-10 22:55:26.47171 INFO::Determining format of input files
2025-09-10 22:55:26.473748 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 22:55:26.481514 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-10 22:55:26.483934 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-10 22:55:26.488033 INFO::Filter data based on min abundance and min prevalence
2025-09-10 22:55:26.489726 INFO::Total samples in data: 1595
2025-09-10 22:55:26.491285 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-10 22:55:26.506704 INFO::Total filtered features: 0
2025-09-10 22:55:26.508794 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 22:55:26.51886 INFO::Total filtered features with variance filtering: 0
2025-09-10 22:55:26.520205 INFO::Filtered feature names from variance filtering:
2025-09-10 22:55:26.521236 INFO::Running selected normalization method: TSS
2025-09-10 22:55:27.720869 INFO::Bypass z-score application to metadata
2025-09-10 22:55:27.722207 INFO::Running selected transform method: AST
2025-09-10 22:55:27.741321 INFO::Running selected analysis method: LM
2025-09-10 22:55:28.421443 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-10 22:55:28.984295 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-10 22:55:29.178185 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-10 22:55:29.358683 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-10 22:55:29.507949 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-10 22:55:29.665112 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-10 22:55:29.838263 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-10 22:55:30.024605 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-10 22:55:30.18773 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-10 22:55:30.357651 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-10 22:55:30.540352 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-10 22:55:30.685767 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-10 22:55:30.846146 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-10 22:55:31.022752 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-10 22:55:31.208949 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-10 22:55:31.379234 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-10 22:55:31.54369 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-10 22:55:31.708553 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-10 22:55:31.876385 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-10 22:55:32.052509 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-10 22:55:32.231217 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-10 22:55:32.405363 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-10 22:55:32.579947 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-10 22:55:32.762127 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-10 22:55:32.924064 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-10 22:55:33.098926 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-10 22:55:33.281619 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-10 22:55:33.449374 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-10 22:55:33.622955 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-10 22:55:33.802815 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-10 22:55:33.969915 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-10 22:55:34.115199 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-10 22:55:34.302557 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-10 22:55:34.479067 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-10 22:55:34.656635 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-10 22:55:34.830585 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-10 22:55:35.017446 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-10 22:55:35.180644 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-10 22:55:35.335145 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-10 22:55:35.493255 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-10 22:55:35.673663 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-10 22:55:35.844125 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-10 22:55:36.016087 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-10 22:55:36.178514 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-10 22:55:36.356363 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-10 22:55:36.51078 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-10 22:55:36.688233 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-10 22:55:36.849092 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-10 22:55:37.029546 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-10 22:55:37.190015 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-10 22:55:37.342537 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-10 22:55:37.520028 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-10 22:55:37.699739 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-10 22:55:37.874269 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-10 22:55:38.068025 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-10 22:55:38.234955 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-10 22:55:38.414588 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-10 22:55:38.607675 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-10 22:55:38.776296 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-10 22:55:38.951859 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-10 22:55:39.116409 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-10 22:55:39.294478 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-10 22:55:39.715776 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-10 22:55:39.878842 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-10 22:55:40.039143 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-10 22:55:40.209586 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-10 22:55:40.383527 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-10 22:55:40.553381 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-10 22:55:40.726376 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-10 22:55:40.901099 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-10 22:55:41.068845 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-10 22:55:41.236912 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-10 22:55:41.401608 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-10 22:55:41.555642 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-10 22:55:41.714632 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-10 22:55:41.880837 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-10 22:55:42.033646 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-10 22:55:42.196326 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-10 22:55:42.370598 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-10 22:55:42.543179 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-10 22:55:42.716933 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-10 22:55:42.903775 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-10 22:55:43.076076 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-10 22:55:43.228859 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-10 22:55:43.396885 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-10 22:55:43.564931 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-10 22:55:43.729444 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-10 22:55:43.868886 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-10 22:55:44.070812 INFO::Counting total values for each feature
2025-09-10 22:55:44.119163 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-10 22:55:44.261265 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-10 22:55:44.422051 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-10 22:55:44.584687 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-10 22:55:44.645499 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-10 22:55:44.675606 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-10 22:55:44.682629 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-10 22:55:44.691261 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"
2025-09-10 22:55:44.708807 INFO::Writing function arguments to log file
2025-09-10 22:55:44.718673 INFO::Verifying options selected are valid
2025-09-10 22:55:44.720227 INFO::Determining format of input files
2025-09-10 22:55:44.722073 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 22:55:44.729715 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-10 22:55:44.731157 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-09-10 22:55:44.733267 INFO::Filter data based on min abundance and min prevalence
2025-09-10 22:55:44.734638 INFO::Total samples in data: 1595
2025-09-10 22:55:44.735949 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-10 22:55:44.741315 INFO::Total filtered features: 0
2025-09-10 22:55:44.743002 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 22:55:44.749572 INFO::Total filtered features with variance filtering: 0
2025-09-10 22:55:44.763021 INFO::Filtered feature names from variance filtering:
2025-09-10 22:55:44.764611 INFO::Running selected normalization method: NONE
2025-09-10 22:55:44.765638 INFO::Bypass z-score application to metadata
2025-09-10 22:55:44.76674 INFO::Running selected transform method: AST
2025-09-10 22:55:44.77973 INFO::Running selected analysis method: LM
2025-09-10 22:55:44.78191 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-10 22:55:44.942461 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-10 22:55:45.108433 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-10 22:55:45.258335 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-10 22:55:45.418148 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-10 22:55:45.567496 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-10 22:55:45.720439 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-10 22:55:45.858865 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-10 22:55:46.016719 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-10 22:55:46.167627 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-10 22:55:46.324478 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-10 22:55:46.467932 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-10 22:55:46.619694 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-10 22:55:46.737993 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-10 22:55:46.906831 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-10 22:55:47.295258 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-10 22:55:47.453247 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-10 22:55:47.603727 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-10 22:55:47.758935 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-10 22:55:47.910293 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-10 22:55:48.046862 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-10 22:55:48.202936 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-10 22:55:48.358173 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-10 22:55:48.52323 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-10 22:55:48.687167 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-10 22:55:48.861421 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-10 22:55:49.039863 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-10 22:55:49.195703 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-10 22:55:49.361108 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-10 22:55:49.526168 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-10 22:55:49.69634 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-10 22:55:49.854451 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-10 22:55:50.006494 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-10 22:55:50.196153 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-10 22:55:50.357306 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-10 22:55:50.527323 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-10 22:55:50.705337 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-10 22:55:50.893409 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-10 22:55:51.068007 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-10 22:55:51.239968 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-10 22:55:51.404417 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-10 22:55:51.583428 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-10 22:55:51.746947 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-10 22:55:51.912767 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-10 22:55:52.078964 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-10 22:55:52.249627 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-10 22:55:52.409334 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-10 22:55:52.58305 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-10 22:55:52.753833 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-10 22:55:52.911412 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-10 22:55:53.075771 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-10 22:55:53.233947 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-10 22:55:53.406384 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-10 22:55:53.56661 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-10 22:55:53.730418 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-10 22:55:53.888652 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-10 22:55:54.03701 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-10 22:55:54.199942 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-10 22:55:54.347875 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-10 22:55:54.501757 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-10 22:55:54.686738 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-10 22:55:54.836727 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-10 22:55:54.99473 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-10 22:55:55.160456 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-10 22:55:55.309336 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-10 22:55:55.473216 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-10 22:55:55.641732 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-10 22:55:55.803022 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-10 22:55:55.94134 WARNING::Fitting problem for feature 67 a warning was issued
2025-09-10 22:55:56.121678 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-10 22:55:56.280085 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-10 22:55:56.443193 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-10 22:55:56.630491 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-10 22:55:56.800415 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-10 22:55:56.863964 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-10 22:55:57.030796 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-10 22:55:57.20417 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-10 22:55:57.364587 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-10 22:55:57.541696 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-10 22:55:57.712882 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-10 22:55:57.872966 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-10 22:55:58.033231 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-10 22:55:58.216074 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-10 22:55:58.357433 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-10 22:55:58.517199 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-10 22:55:58.696244 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-10 22:55:58.844244 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-10 22:55:59.001111 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-10 22:55:59.160171 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-10 22:55:59.329449 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-10 22:55:59.519333 INFO::Counting total values for each feature
2025-09-10 22:55:59.542934 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-10 22:55:59.676423 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-10 22:55:59.798574 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-10 22:55:59.959929 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-10 22:56:00.03116 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-10 22:56:00.351619 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-10 22:56:00.359414 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-10 22:56:00.366444 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 34.594   0.724  35.530

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 98.974 1.772101.494