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This page was generated on 2026-03-23 11:35 -0400 (Mon, 23 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4868
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" 4548
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 1175/2368HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.25.1  (landing page)
Sagun Maharjan
Snapshot Date: 2026-03-22 13:40 -0400 (Sun, 22 Mar 2026)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 05f7fa4
git_last_commit_date: 2026-02-27 02:44:53 -0400 (Fri, 27 Feb 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
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: 1.25.1
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: 2026-03-22 20:25:23 -0400 (Sun, 22 Mar 2026)
EndedAt: 2026-03-22 20:26:37 -0400 (Sun, 22 Mar 2026)
EllapsedTime: 73.8 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_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* 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: 2026-03-23 00:25:23 UTC
* 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 40.94  0.626  41.888
* 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 ‘1.25.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.19
Current TMB package version is 1.9.20
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** 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) (2026-03-20 r89666) -- "Unsuffered Consequences"
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"
2026-03-22 20:26:21.344485 INFO::Writing function arguments to log file
2026-03-22 20:26:21.363156 INFO::Verifying options selected are valid
2026-03-22 20:26:21.377239 INFO::Determining format of input files
2026-03-22 20:26:21.37815 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-22 20:26:21.380742 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-22 20:26:21.381357 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-03-22 20:26:21.382497 INFO::Filter data based on min abundance and min prevalence
2026-03-22 20:26:21.383193 INFO::Total samples in data: 1595
2026-03-22 20:26:21.38434 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-22 20:26:21.387017 INFO::Total filtered features: 0
2026-03-22 20:26:21.387688 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-22 20:26:21.393064 INFO::Total filtered features with variance filtering: 0
2026-03-22 20:26:21.393902 INFO::Filtered feature names from variance filtering:
2026-03-22 20:26:21.394534 INFO::Running selected normalization method: TSS
2026-03-22 20:26:21.822793 INFO::Bypass z-score application to metadata
2026-03-22 20:26:21.823437 INFO::Running selected transform method: AST
2026-03-22 20:26:21.828984 INFO::Running selected analysis method: LM
2026-03-22 20:26:22.089908 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-22 20:26:22.355251 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-22 20:26:22.418511 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-22 20:26:22.473976 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-22 20:26:22.527325 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-22 20:26:22.585616 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-22 20:26:22.639875 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-22 20:26:22.700565 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-22 20:26:22.783858 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-22 20:26:22.835775 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-22 20:26:22.890931 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-22 20:26:22.965991 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-22 20:26:23.01693 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-22 20:26:23.059177 WARNING::Fitting problem for feature 13 a warning was issued
2026-03-22 20:26:23.118611 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-22 20:26:23.169922 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-22 20:26:23.223086 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-22 20:26:23.276153 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-22 20:26:23.331267 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-22 20:26:23.383779 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-22 20:26:23.450282 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-22 20:26:23.51741 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-22 20:26:23.568426 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-22 20:26:23.624838 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-22 20:26:23.675254 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-22 20:26:23.731322 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-22 20:26:23.788227 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-22 20:26:23.852635 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-22 20:26:23.908869 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-22 20:26:24.077574 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-22 20:26:24.131412 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-22 20:26:24.183301 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-22 20:26:24.240828 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-22 20:26:24.302729 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-22 20:26:24.357394 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-22 20:26:24.405205 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-22 20:26:24.458284 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-22 20:26:24.512758 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-22 20:26:24.566562 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-22 20:26:24.614645 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-22 20:26:24.665096 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-22 20:26:24.720023 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-22 20:26:24.772305 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-22 20:26:24.827 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-22 20:26:24.883538 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-22 20:26:24.936495 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-22 20:26:24.987033 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-22 20:26:25.037796 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-22 20:26:25.091894 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-22 20:26:25.146438 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-22 20:26:25.199045 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-22 20:26:25.250609 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-22 20:26:25.310205 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-22 20:26:25.361272 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-22 20:26:25.415486 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-22 20:26:25.472337 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-22 20:26:25.531722 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-22 20:26:25.589103 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-22 20:26:25.643095 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-22 20:26:25.69694 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-22 20:26:25.75419 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-22 20:26:25.810432 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-22 20:26:25.86381 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-22 20:26:25.916268 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-22 20:26:25.970448 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-22 20:26:26.021025 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-22 20:26:26.071091 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-22 20:26:26.122403 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-22 20:26:26.172885 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-22 20:26:26.224253 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-22 20:26:26.282322 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-22 20:26:26.340375 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-22 20:26:26.396754 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-22 20:26:26.453706 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-22 20:26:26.503745 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-22 20:26:26.574139 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-22 20:26:26.644181 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-22 20:26:26.69634 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-22 20:26:26.750497 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-22 20:26:26.810187 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-22 20:26:26.870284 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-22 20:26:26.930887 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-22 20:26:27.001311 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-22 20:26:27.09488 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-22 20:26:27.14948 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-22 20:26:27.200451 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-22 20:26:27.24969 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-22 20:26:27.303633 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-22 20:26:27.371321 INFO::Counting total values for each feature
2026-03-22 20:26:27.38297 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-03-22 20:26:27.43033 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-03-22 20:26:27.486124 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-03-22 20:26:27.55336 INFO::Writing residuals to file output/fits/residuals.rds
2026-03-22 20:26:27.585536 INFO::Writing fitted values to file output/fits/fitted.rds
2026-03-22 20:26:27.599235 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-03-22 20:26:27.602448 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-03-22 20:26:27.607051 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"
2026-03-22 20:26:27.615129 INFO::Writing function arguments to log file
2026-03-22 20:26:27.619676 INFO::Verifying options selected are valid
2026-03-22 20:26:27.620249 INFO::Determining format of input files
2026-03-22 20:26:27.62124 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-22 20:26:27.62475 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-22 20:26:27.625336 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-03-22 20:26:27.626192 INFO::Filter data based on min abundance and min prevalence
2026-03-22 20:26:27.626711 INFO::Total samples in data: 1595
2026-03-22 20:26:27.627204 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-22 20:26:27.629319 INFO::Total filtered features: 0
2026-03-22 20:26:27.629933 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-22 20:26:27.632658 INFO::Total filtered features with variance filtering: 0
2026-03-22 20:26:27.63347 INFO::Filtered feature names from variance filtering:
2026-03-22 20:26:27.634111 INFO::Running selected normalization method: NONE
2026-03-22 20:26:27.634624 INFO::Bypass z-score application to metadata
2026-03-22 20:26:27.635116 INFO::Running selected transform method: AST
2026-03-22 20:26:27.643 INFO::Running selected analysis method: LM
2026-03-22 20:26:27.643951 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-22 20:26:27.698555 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-22 20:26:27.753402 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-22 20:26:27.806314 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-22 20:26:27.856163 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-22 20:26:27.907932 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-22 20:26:27.958527 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-22 20:26:28.014094 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-22 20:26:28.06354 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-22 20:26:28.134335 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-22 20:26:28.188803 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-22 20:26:28.244546 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-22 20:26:28.293515 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-22 20:26:28.349558 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-22 20:26:28.407958 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-22 20:26:28.476436 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-22 20:26:28.519257 WARNING::Fitting problem for feature 16 a warning was issued
2026-03-22 20:26:28.574707 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-22 20:26:28.62739 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-22 20:26:28.818265 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-22 20:26:28.875889 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-22 20:26:28.931283 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-22 20:26:29.003732 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-22 20:26:29.075432 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-22 20:26:29.123218 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-22 20:26:29.175572 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-22 20:26:29.224562 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-22 20:26:29.289961 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-22 20:26:29.343758 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-22 20:26:29.394847 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-22 20:26:29.443622 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-22 20:26:29.499204 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-22 20:26:29.550334 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-22 20:26:29.609896 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-22 20:26:29.668587 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-22 20:26:29.736073 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-22 20:26:29.786034 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-22 20:26:29.835227 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-22 20:26:29.886184 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-22 20:26:29.941929 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-22 20:26:29.988932 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-22 20:26:30.036831 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-22 20:26:30.085418 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-22 20:26:30.13493 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-22 20:26:30.191321 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-22 20:26:30.24403 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-22 20:26:30.302516 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-22 20:26:30.354375 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-22 20:26:30.408498 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-22 20:26:30.462036 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-22 20:26:30.516952 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-22 20:26:30.56264 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-22 20:26:30.616116 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-22 20:26:30.661402 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-22 20:26:30.697689 WARNING::Fitting problem for feature 53 a warning was issued
2026-03-22 20:26:30.745739 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-22 20:26:30.803743 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-22 20:26:30.85316 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-22 20:26:30.903032 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-22 20:26:30.958894 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-22 20:26:31.012102 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-22 20:26:31.063459 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-22 20:26:31.111423 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-22 20:26:31.161488 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-22 20:26:31.21263 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-22 20:26:31.261845 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-22 20:26:31.311432 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-22 20:26:31.360147 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-22 20:26:31.413461 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-22 20:26:31.462643 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-22 20:26:31.511592 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-22 20:26:31.564522 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-22 20:26:31.622667 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-22 20:26:31.672698 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-22 20:26:31.690984 WARNING::Fitting problem for feature 72 a warning was issued
2026-03-22 20:26:31.742749 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-22 20:26:31.793462 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-22 20:26:31.8502 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-22 20:26:31.903751 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-22 20:26:31.965062 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-22 20:26:32.014437 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-22 20:26:32.071041 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-22 20:26:32.124232 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-22 20:26:32.174667 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-22 20:26:32.233457 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-22 20:26:32.283197 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-22 20:26:32.333542 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-22 20:26:32.381752 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-22 20:26:32.549082 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-22 20:26:32.612782 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-22 20:26:32.672071 INFO::Counting total values for each feature
2026-03-22 20:26:32.680572 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-03-22 20:26:32.728331 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-03-22 20:26:32.777403 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-03-22 20:26:32.839195 INFO::Writing residuals to file output2/fits/residuals.rds
2026-03-22 20:26:32.875489 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-03-22 20:26:32.909967 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-03-22 20:26:32.913206 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-03-22 20:26:32.915643 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 
 11.766   0.265  12.128

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin240.940 0.62641.888