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This page was generated on 2026-05-26 11:36 -0400 (Tue, 26 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4938
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-05-01 r89994) -- "Because it was There" 4640
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 1184/2379HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.27.0  (landing page)
Sagun Maharjan
Snapshot Date: 2026-05-25 13:45 -0400 (Mon, 25 May 2026)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 6335054
git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (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  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: 1.27.0
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_1.27.0.tar.gz
StartedAt: 2026-05-25 20:13:38 -0400 (Mon, 25 May 2026)
EndedAt: 2026-05-25 20:14:49 -0400 (Mon, 25 May 2026)
EllapsedTime: 70.9 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* 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: 2026-05-26 00:13:39 UTC
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.27.0’
* 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 40.181  0.567  40.947
* 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-3.24-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 ‘1.27.0’
** 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 (2026-05-01 r89994) -- "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"
2026-05-25 20:14:35.308123 INFO::Writing function arguments to log file
2026-05-25 20:14:35.318812 INFO::Verifying options selected are valid
2026-05-25 20:14:35.332186 INFO::Determining format of input files
2026-05-25 20:14:35.333052 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-25 20:14:35.335596 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-25 20:14:35.336274 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-25 20:14:35.339869 INFO::Filter data based on min abundance and min prevalence
2026-05-25 20:14:35.340398 INFO::Total samples in data: 1595
2026-05-25 20:14:35.340786 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-25 20:14:35.342388 INFO::Total filtered features: 0
2026-05-25 20:14:35.342915 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-25 20:14:35.345836 INFO::Total filtered features with variance filtering: 0
2026-05-25 20:14:35.346372 INFO::Filtered feature names from variance filtering:
2026-05-25 20:14:35.346783 INFO::Running selected normalization method: TSS
2026-05-25 20:14:35.757239 INFO::Bypass z-score application to metadata
2026-05-25 20:14:35.757953 INFO::Running selected transform method: AST
2026-05-25 20:14:35.767489 INFO::Running selected analysis method: LM
2026-05-25 20:14:36.011598 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-25 20:14:36.235499 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-25 20:14:36.29756 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-25 20:14:36.348497 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-25 20:14:36.400633 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-25 20:14:36.457595 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-25 20:14:36.508532 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-25 20:14:36.565568 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-25 20:14:36.623764 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-25 20:14:36.674881 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-25 20:14:36.724899 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-25 20:14:36.795344 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-25 20:14:36.845054 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-25 20:14:36.896293 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-25 20:14:36.948625 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-25 20:14:37.004918 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-25 20:14:37.056107 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-25 20:14:37.110317 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-25 20:14:37.16525 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-25 20:14:37.211581 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-25 20:14:37.260286 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-25 20:14:37.31619 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-25 20:14:37.368572 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-25 20:14:37.417974 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-25 20:14:37.474087 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-25 20:14:37.525923 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-25 20:14:37.574969 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-25 20:14:37.639206 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-25 20:14:37.693977 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-25 20:14:37.751289 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-25 20:14:37.806301 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-25 20:14:37.859583 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-25 20:14:37.910916 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-25 20:14:37.972252 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-25 20:14:38.02645 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-25 20:14:38.088775 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-25 20:14:38.143228 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-25 20:14:38.197877 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-25 20:14:38.252955 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-25 20:14:38.30418 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-25 20:14:38.37589 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-25 20:14:38.424699 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-25 20:14:38.476908 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-25 20:14:38.533482 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-25 20:14:38.584879 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-25 20:14:38.635288 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-25 20:14:38.691334 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-25 20:14:38.74658 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-25 20:14:38.797627 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-25 20:14:38.85113 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-25 20:14:38.900431 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-25 20:14:38.951178 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-25 20:14:39.007111 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-25 20:14:39.061778 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-25 20:14:39.109429 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-25 20:14:39.167264 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-25 20:14:39.222253 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-25 20:14:39.276324 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-25 20:14:39.329443 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-25 20:14:39.379239 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-25 20:14:39.431298 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-25 20:14:39.481775 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-25 20:14:39.535473 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-25 20:14:39.585506 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-25 20:14:39.634401 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-25 20:14:39.687246 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-25 20:14:39.739817 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-25 20:14:39.79306 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-25 20:14:39.845722 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-25 20:14:39.908307 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-25 20:14:39.963975 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-25 20:14:40.125568 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-25 20:14:40.177256 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-25 20:14:40.226939 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-25 20:14:40.278289 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-25 20:14:40.335193 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-25 20:14:40.386932 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-25 20:14:40.440216 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-25 20:14:40.501421 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-25 20:14:40.556638 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-25 20:14:40.609983 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-25 20:14:40.66516 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-25 20:14:40.721394 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-25 20:14:40.774941 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-25 20:14:40.827354 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-25 20:14:40.879708 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-25 20:14:40.928515 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-25 20:14:40.995322 INFO::Counting total values for each feature
2026-05-25 20:14:41.007884 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-25 20:14:41.05519 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-25 20:14:41.110111 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-25 20:14:41.16517 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-25 20:14:41.192114 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-25 20:14:41.205732 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-25 20:14:41.208889 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-25 20:14:41.215422 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"
2026-05-25 20:14:41.221383 INFO::Writing function arguments to log file
2026-05-25 20:14:41.22463 INFO::Verifying options selected are valid
2026-05-25 20:14:41.225048 INFO::Determining format of input files
2026-05-25 20:14:41.225562 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-25 20:14:41.227815 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-25 20:14:41.228275 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-05-25 20:14:41.228912 INFO::Filter data based on min abundance and min prevalence
2026-05-25 20:14:41.229286 INFO::Total samples in data: 1595
2026-05-25 20:14:41.22964 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-25 20:14:41.231092 INFO::Total filtered features: 0
2026-05-25 20:14:41.231501 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-25 20:14:41.234058 INFO::Total filtered features with variance filtering: 0
2026-05-25 20:14:41.234532 INFO::Filtered feature names from variance filtering:
2026-05-25 20:14:41.234955 INFO::Running selected normalization method: NONE
2026-05-25 20:14:41.235318 INFO::Bypass z-score application to metadata
2026-05-25 20:14:41.235666 INFO::Running selected transform method: AST
2026-05-25 20:14:41.241148 INFO::Running selected analysis method: LM
2026-05-25 20:14:41.241806 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-25 20:14:41.291861 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-25 20:14:41.343616 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-25 20:14:41.393309 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-25 20:14:41.443194 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-25 20:14:41.494375 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-25 20:14:41.553257 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-25 20:14:41.607407 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-25 20:14:41.657177 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-25 20:14:41.708893 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-25 20:14:41.76475 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-25 20:14:41.815428 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-25 20:14:41.8627 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-25 20:14:41.912206 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-25 20:14:41.964886 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-25 20:14:42.017181 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-25 20:14:42.063202 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-25 20:14:42.119037 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-25 20:14:42.167577 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-25 20:14:42.21397 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-25 20:14:42.263055 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-25 20:14:42.318329 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-25 20:14:42.369686 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-25 20:14:42.417713 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-25 20:14:42.469611 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-25 20:14:42.522496 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-25 20:14:42.572521 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-25 20:14:42.624906 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-25 20:14:42.679194 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-25 20:14:42.726408 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-25 20:14:42.776081 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-25 20:14:42.827128 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-25 20:14:42.883705 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-25 20:14:42.934515 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-25 20:14:42.985884 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-25 20:14:43.039364 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-25 20:14:43.091036 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-25 20:14:43.142041 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-25 20:14:43.198264 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-25 20:14:43.244376 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-25 20:14:43.29282 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-25 20:14:43.343901 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-25 20:14:43.390908 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-25 20:14:43.444536 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-25 20:14:43.499855 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-25 20:14:43.551126 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-25 20:14:43.601958 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-25 20:14:43.654012 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-25 20:14:43.707199 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-25 20:14:43.759799 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-25 20:14:43.804239 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-25 20:14:43.852591 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-25 20:14:43.907188 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-25 20:14:43.951754 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-25 20:14:44.001026 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-25 20:14:44.053016 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-25 20:14:44.110006 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-25 20:14:44.162081 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-25 20:14:44.21616 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-25 20:14:44.272622 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-25 20:14:44.320475 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-25 20:14:44.370219 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-25 20:14:44.418714 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-25 20:14:44.473931 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-25 20:14:44.522937 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-25 20:14:44.575012 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-25 20:14:44.626161 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-25 20:14:44.678754 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-25 20:14:44.725743 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-25 20:14:44.776807 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-25 20:14:44.831683 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-25 20:14:44.886529 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-25 20:14:44.904762 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-25 20:14:44.958301 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-25 20:14:45.008079 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-25 20:14:45.057787 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-25 20:14:45.108134 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-25 20:14:45.159356 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-25 20:14:45.208209 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-25 20:14:45.262696 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-25 20:14:45.312743 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-25 20:14:45.362294 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-25 20:14:45.422827 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-25 20:14:45.471425 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-25 20:14:45.515851 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-25 20:14:45.558096 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-25 20:14:45.605127 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-25 20:14:45.655368 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-25 20:14:45.712969 INFO::Counting total values for each feature
2026-05-25 20:14:45.725449 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-25 20:14:45.772656 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-25 20:14:45.819727 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-25 20:14:45.871162 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-25 20:14:45.9039 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-25 20:14:45.938595 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-25 20:14:45.942125 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-25 20:14:45.945198 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 
 10.911   0.193  11.132

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin240.181 0.56740.947