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This page was generated on 2025-09-11 12:06 -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 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: 1.23.0
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 21:05:38 -0400 (Wed, 10 Sep 2025)
EndedAt: 2025-09-10 21:06:37 -0400 (Wed, 10 Sep 2025)
EllapsedTime: 58.8 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_1.23.0.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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 29.953  0.578  30.678
* 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-arm64/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: aarch64-apple-darwin20

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

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

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

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-09-10 21:06:23.212947 INFO::Writing function arguments to log file
2025-09-10 21:06:23.23089 INFO::Verifying options selected are valid
2025-09-10 21:06:23.244547 INFO::Determining format of input files
2025-09-10 21:06:23.245241 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 21:06:23.247399 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-10 21:06:23.247891 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-10 21:06:23.248714 INFO::Filter data based on min abundance and min prevalence
2025-09-10 21:06:23.249026 INFO::Total samples in data: 1595
2025-09-10 21:06:23.249311 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-10 21:06:23.254244 INFO::Total filtered features: 0
2025-09-10 21:06:23.254774 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 21:06:23.258039 INFO::Total filtered features with variance filtering: 0
2025-09-10 21:06:23.258455 INFO::Filtered feature names from variance filtering:
2025-09-10 21:06:23.258758 INFO::Running selected normalization method: TSS
2025-09-10 21:06:23.663328 INFO::Bypass z-score application to metadata
2025-09-10 21:06:23.663816 INFO::Running selected transform method: AST
2025-09-10 21:06:23.669904 INFO::Running selected analysis method: LM
2025-09-10 21:06:23.891726 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-10 21:06:24.054604 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-10 21:06:24.107241 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-10 21:06:24.16623 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-10 21:06:24.219141 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-10 21:06:24.272151 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-10 21:06:24.324929 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-10 21:06:24.381448 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-10 21:06:24.42461 WARNING::Fitting problem for feature 8 a warning was issued
2025-09-10 21:06:24.480065 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-10 21:06:24.527806 WARNING::Fitting problem for feature 9 a warning was issued
2025-09-10 21:06:24.584889 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-10 21:06:24.637631 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-10 21:06:24.713822 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-10 21:06:24.766976 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-10 21:06:24.822155 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-10 21:06:24.875833 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-10 21:06:24.934622 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-10 21:06:24.988533 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-10 21:06:25.045398 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-10 21:06:25.103523 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-10 21:06:25.152408 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-10 21:06:25.203512 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-10 21:06:25.363793 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-10 21:06:25.414488 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-10 21:06:25.466972 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-10 21:06:25.535671 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-10 21:06:25.594524 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-10 21:06:25.643905 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-10 21:06:25.698363 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-10 21:06:25.756271 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-10 21:06:25.813019 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-10 21:06:25.863441 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-10 21:06:25.920598 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-10 21:06:25.971596 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-10 21:06:26.025725 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-10 21:06:26.079438 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-10 21:06:26.129746 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-10 21:06:26.18052 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-10 21:06:26.242549 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-10 21:06:26.292504 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-10 21:06:26.343059 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-10 21:06:26.401613 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-10 21:06:26.454919 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-10 21:06:26.512448 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-10 21:06:26.567935 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-10 21:06:26.61878 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-10 21:06:26.676026 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-10 21:06:26.735992 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-10 21:06:26.793178 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-10 21:06:26.844149 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-10 21:06:26.899772 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-10 21:06:26.950133 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-10 21:06:27.004678 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-10 21:06:27.056995 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-10 21:06:27.111623 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-10 21:06:27.164306 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-10 21:06:27.217113 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-10 21:06:27.275602 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-10 21:06:27.324244 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-10 21:06:27.378996 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-10 21:06:27.428237 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-10 21:06:27.480797 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-10 21:06:27.53065 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-10 21:06:27.587745 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-10 21:06:27.638532 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-10 21:06:27.692767 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-10 21:06:27.741309 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-10 21:06:27.793536 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-10 21:06:27.842217 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-10 21:06:27.891942 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-10 21:06:27.95148 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-10 21:06:28.004518 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-10 21:06:28.053654 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-10 21:06:28.10844 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-10 21:06:28.158118 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-10 21:06:28.209775 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-10 21:06:28.268391 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-10 21:06:28.323175 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-10 21:06:28.376351 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-10 21:06:28.435473 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-10 21:06:28.488335 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-10 21:06:28.538653 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-10 21:06:28.595934 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-10 21:06:28.647897 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-10 21:06:28.696147 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-10 21:06:28.751709 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-10 21:06:28.801724 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-10 21:06:28.854156 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-10 21:06:28.927289 INFO::Counting total values for each feature
2025-09-10 21:06:28.940489 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-10 21:06:28.990849 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-10 21:06:29.049874 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-10 21:06:29.113011 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-10 21:06:29.140257 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-10 21:06:29.155127 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-10 21:06:29.158333 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-10 21:06:29.161492 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 21:06:29.16749 INFO::Writing function arguments to log file
2025-09-10 21:06:29.16978 INFO::Verifying options selected are valid
2025-09-10 21:06:29.170162 INFO::Determining format of input files
2025-09-10 21:06:29.170596 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 21:06:29.172626 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-10 21:06:29.173023 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-09-10 21:06:29.173617 INFO::Filter data based on min abundance and min prevalence
2025-09-10 21:06:29.173905 INFO::Total samples in data: 1595
2025-09-10 21:06:29.174177 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-10 21:06:29.175746 INFO::Total filtered features: 0
2025-09-10 21:06:29.176128 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 21:06:29.179263 INFO::Total filtered features with variance filtering: 0
2025-09-10 21:06:29.179598 INFO::Filtered feature names from variance filtering:
2025-09-10 21:06:29.179856 INFO::Running selected normalization method: NONE
2025-09-10 21:06:29.180104 INFO::Bypass z-score application to metadata
2025-09-10 21:06:29.180348 INFO::Running selected transform method: AST
2025-09-10 21:06:29.186375 INFO::Running selected analysis method: LM
2025-09-10 21:06:29.186899 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-10 21:06:29.242088 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-10 21:06:29.292809 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-10 21:06:29.343716 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-10 21:06:29.396692 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-10 21:06:29.445506 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-10 21:06:29.50133 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-10 21:06:29.550981 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-10 21:06:29.604696 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-10 21:06:29.646821 WARNING::Fitting problem for feature 9 a warning was issued
2025-09-10 21:06:29.702811 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-10 21:06:29.86271 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-10 21:06:29.915364 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-10 21:06:29.966664 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-10 21:06:30.011376 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-10 21:06:30.06977 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-10 21:06:30.119851 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-10 21:06:30.170857 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-10 21:06:30.211717 WARNING::Fitting problem for feature 16 a warning was issued
2025-09-10 21:06:30.266917 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-10 21:06:30.318443 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-10 21:06:30.368409 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-10 21:06:30.420775 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-10 21:06:30.469578 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-10 21:06:30.520298 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-10 21:06:30.570941 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-10 21:06:30.717253 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-10 21:06:30.767968 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-10 21:06:30.817911 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-10 21:06:30.867722 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-10 21:06:30.923545 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-10 21:06:30.971131 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-10 21:06:31.019148 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-10 21:06:31.072747 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-10 21:06:31.121705 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-10 21:06:31.173864 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-10 21:06:31.223608 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-10 21:06:31.27904 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-10 21:06:31.329233 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-10 21:06:31.388463 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-10 21:06:31.441225 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-10 21:06:31.501459 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-10 21:06:31.550492 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-10 21:06:31.603888 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-10 21:06:31.666627 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-10 21:06:31.71729 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-10 21:06:31.774697 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-10 21:06:31.830052 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-10 21:06:31.884865 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-10 21:06:31.9362 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-10 21:06:31.984586 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-10 21:06:32.040034 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-10 21:06:32.089538 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-10 21:06:32.137214 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-10 21:06:32.189137 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-10 21:06:32.241841 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-10 21:06:32.28997 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-10 21:06:32.339754 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-10 21:06:32.394623 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-10 21:06:32.443889 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-10 21:06:32.494391 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-10 21:06:32.549173 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-10 21:06:32.60139 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-10 21:06:32.651175 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-10 21:06:32.69975 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-10 21:06:32.751998 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-10 21:06:32.803091 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-10 21:06:32.853 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-10 21:06:32.906315 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-10 21:06:32.956348 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-10 21:06:33.008207 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-10 21:06:33.062728 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-10 21:06:33.11534 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-10 21:06:33.169366 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-10 21:06:33.225837 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-10 21:06:33.245138 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-10 21:06:33.295632 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-10 21:06:33.350064 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-10 21:06:33.400168 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-10 21:06:33.450207 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-10 21:06:33.50648 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-10 21:06:33.554835 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-10 21:06:33.6076 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-10 21:06:33.658135 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-10 21:06:33.70808 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-10 21:06:33.76374 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-10 21:06:33.811657 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-10 21:06:33.86328 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-10 21:06:33.911814 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-10 21:06:33.965508 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-10 21:06:34.017225 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-10 21:06:34.080864 INFO::Counting total values for each feature
2025-09-10 21:06:34.089697 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-10 21:06:34.140679 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-10 21:06:34.190939 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-10 21:06:34.250209 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-10 21:06:34.287156 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-10 21:06:34.321743 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-10 21:06:34.324887 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-10 21:06:34.327268 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 11.181   0.316  11.545

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin229.953 0.57830.678