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This page was generated on 2025-09-11 11:38 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
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 1154/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.22.0  (landing page)
Lauren McIver
Snapshot Date: 2025-09-08 13:40 -0400 (Mon, 08 Sep 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_21
git_last_commit: fcec85e
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on nebbiolo1

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: 1.22.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.22.0.tar.gz
StartedAt: 2025-09-11 01:16:07 -0400 (Thu, 11 Sep 2025)
EndedAt: 2025-09-11 01:20:20 -0400 (Thu, 11 Sep 2025)
EllapsedTime: 253.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* 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 loading without being on the library search path ... 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 88.795  1.632  90.444
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.22.0’
** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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"
2025-09-11 01:18:07.132402 INFO::Writing function arguments to log file
2025-09-11 01:18:07.170948 INFO::Verifying options selected are valid
2025-09-11 01:18:07.204068 INFO::Determining format of input files
2025-09-11 01:18:07.205559 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 01:18:07.210512 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-11 01:18:07.21179 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-11 01:18:07.214115 INFO::Filter data based on min abundance and min prevalence
2025-09-11 01:18:07.215026 INFO::Total samples in data: 1595
2025-09-11 01:18:07.215882 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-11 01:18:07.226647 INFO::Total filtered features: 0
2025-09-11 01:18:07.227842 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-11 01:18:07.234295 INFO::Total filtered features with variance filtering: 0
2025-09-11 01:18:07.235317 INFO::Filtered feature names from variance filtering:
2025-09-11 01:18:07.236195 INFO::Running selected normalization method: TSS
2025-09-11 01:18:08.297642 INFO::Bypass z-score application to metadata
2025-09-11 01:18:08.299161 INFO::Running selected transform method: AST
2025-09-11 01:18:08.3161 INFO::Running selected analysis method: LM
2025-09-11 01:18:08.927155 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-11 01:18:09.389493 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-11 01:18:09.538569 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-11 01:18:09.699384 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-11 01:18:09.847854 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-11 01:18:09.992594 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-11 01:18:10.138386 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-11 01:18:10.294333 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-11 01:18:10.412252 WARNING::Fitting problem for feature 8 a warning was issued
2025-09-11 01:18:10.563983 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-11 01:18:10.682864 WARNING::Fitting problem for feature 9 a warning was issued
2025-09-11 01:18:10.836175 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-11 01:18:10.975944 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-11 01:18:11.153808 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-11 01:18:11.292568 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-11 01:18:11.413335 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-11 01:18:11.566576 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-11 01:18:11.724254 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-11 01:18:11.890675 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-11 01:18:12.049854 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-11 01:18:12.217105 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-11 01:18:12.369112 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-11 01:18:12.504277 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-11 01:18:12.653213 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-11 01:18:12.798321 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-11 01:18:12.941174 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-11 01:18:13.080186 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-11 01:18:13.233025 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-11 01:18:13.379401 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-11 01:18:13.529546 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-11 01:18:13.692662 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-11 01:18:13.847477 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-11 01:18:14.001446 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-11 01:18:14.158291 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-11 01:18:14.310315 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-11 01:18:14.461321 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-11 01:18:14.621386 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-11 01:18:14.762061 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-11 01:18:14.911714 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-11 01:18:15.053463 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-11 01:18:15.198055 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-11 01:18:15.375475 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-11 01:18:15.525652 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-11 01:18:15.68101 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-11 01:18:15.840135 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-11 01:18:15.987391 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-11 01:18:16.141258 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-11 01:18:16.280691 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-11 01:18:16.424502 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-11 01:18:16.58532 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-11 01:18:16.739349 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-11 01:18:16.894021 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-11 01:18:17.041185 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-11 01:18:17.202069 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-11 01:18:17.350785 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-11 01:18:17.503264 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-11 01:18:17.656205 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-11 01:18:17.80114 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-11 01:18:17.947238 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-11 01:18:18.105787 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-11 01:18:18.245612 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-11 01:18:18.405161 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-11 01:18:18.549943 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-11 01:18:18.703563 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-11 01:18:18.857969 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-11 01:18:19.015788 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-11 01:18:19.199096 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-11 01:18:19.343072 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-11 01:18:19.486272 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-11 01:18:19.646298 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-11 01:18:19.786543 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-11 01:18:19.941901 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-11 01:18:20.092328 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-11 01:18:20.249543 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-11 01:18:20.393279 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-11 01:18:20.553003 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-11 01:18:20.731584 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-11 01:18:20.883318 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-11 01:18:21.03634 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-11 01:18:21.198557 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-11 01:18:21.36057 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-11 01:18:21.51998 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-11 01:18:21.678385 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-11 01:18:21.826579 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-11 01:18:21.982283 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-11 01:18:22.129403 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-11 01:18:22.270435 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-11 01:18:22.42392 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-11 01:18:22.566368 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-11 01:18:22.709173 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-11 01:18:22.911305 INFO::Counting total values for each feature
2025-09-11 01:18:22.946891 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-11 01:18:23.04165 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-11 01:18:23.137529 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-11 01:18:23.237027 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-11 01:18:23.286714 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-11 01:18:23.558385 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-11 01:18:23.564841 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-11 01:18:23.569982 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"
2025-09-11 01:18:23.581657 INFO::Writing function arguments to log file
2025-09-11 01:18:23.587317 INFO::Verifying options selected are valid
2025-09-11 01:18:23.588298 INFO::Determining format of input files
2025-09-11 01:18:23.589461 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 01:18:23.594368 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-11 01:18:23.595411 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-09-11 01:18:23.597039 INFO::Filter data based on min abundance and min prevalence
2025-09-11 01:18:23.597913 INFO::Total samples in data: 1595
2025-09-11 01:18:23.598792 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-11 01:18:23.602839 INFO::Total filtered features: 0
2025-09-11 01:18:23.603795 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-11 01:18:23.61002 INFO::Total filtered features with variance filtering: 0
2025-09-11 01:18:23.611057 INFO::Filtered feature names from variance filtering:
2025-09-11 01:18:23.611908 INFO::Running selected normalization method: NONE
2025-09-11 01:18:23.612751 INFO::Bypass z-score application to metadata
2025-09-11 01:18:23.613567 INFO::Running selected transform method: AST
2025-09-11 01:18:23.626681 INFO::Running selected analysis method: LM
2025-09-11 01:18:23.628182 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-11 01:18:23.763126 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-11 01:18:23.903088 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-11 01:18:24.033614 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-11 01:18:24.1714 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-11 01:18:24.304085 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-11 01:18:24.455064 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-11 01:18:24.596286 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-11 01:18:24.735757 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-11 01:18:24.877045 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-11 01:18:25.01584 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-11 01:18:25.129487 WARNING::Fitting problem for feature 11 a warning was issued
2025-09-11 01:18:25.275422 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-11 01:18:25.414383 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-11 01:18:25.551156 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-11 01:18:25.684196 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-11 01:18:25.829711 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-11 01:18:25.94119 WARNING::Fitting problem for feature 16 a warning was issued
2025-09-11 01:18:26.083267 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-11 01:18:26.230009 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-11 01:18:26.36483 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-11 01:18:26.499937 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-11 01:18:26.646235 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-11 01:18:26.783061 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-11 01:18:26.920125 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-11 01:18:27.058951 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-11 01:18:27.198155 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-11 01:18:27.337579 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-11 01:18:27.478816 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-11 01:18:27.621974 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-11 01:18:27.760639 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-11 01:18:27.889495 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-11 01:18:28.024107 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-11 01:18:28.400302 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-11 01:18:28.544462 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-11 01:18:28.68508 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-11 01:18:28.829329 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-11 01:18:28.967781 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-11 01:18:29.102324 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-11 01:18:29.237123 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-11 01:18:29.37119 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-11 01:18:29.503861 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-11 01:18:29.633101 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-11 01:18:29.765606 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-11 01:18:29.907338 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-11 01:18:30.045699 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-11 01:18:30.188508 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-11 01:18:30.327312 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-11 01:18:30.472902 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-11 01:18:30.604512 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-11 01:18:30.742785 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-11 01:18:30.876554 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-11 01:18:31.012177 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-11 01:18:31.150269 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-11 01:18:31.279591 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-11 01:18:31.416272 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-11 01:18:31.54839 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-11 01:18:31.682237 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-11 01:18:31.82117 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-11 01:18:31.967393 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-11 01:18:32.106659 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-11 01:18:32.248402 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-11 01:18:32.386962 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-11 01:18:32.521195 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-11 01:18:32.658268 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-11 01:18:32.804508 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-11 01:18:32.939536 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-11 01:18:33.077028 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-11 01:18:33.215036 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-11 01:18:33.325967 WARNING::Fitting problem for feature 67 a warning was issued
2025-09-11 01:18:33.469766 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-11 01:18:33.610389 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-11 01:18:33.748739 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-11 01:18:33.90417 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-11 01:18:34.315297 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-11 01:18:34.363422 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-11 01:18:34.497428 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-11 01:18:34.635164 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-11 01:18:34.778172 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-11 01:18:34.920814 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-11 01:18:35.059389 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-11 01:18:35.195779 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-11 01:18:35.337526 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-11 01:18:35.486249 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-11 01:18:35.621692 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-11 01:18:35.767315 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-11 01:18:35.905633 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-11 01:18:36.039738 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-11 01:18:36.170506 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-11 01:18:36.305252 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-11 01:18:36.445939 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-11 01:18:36.612424 INFO::Counting total values for each feature
2025-09-11 01:18:36.633544 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-11 01:18:36.726096 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-11 01:18:36.819072 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-11 01:18:36.916071 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-11 01:18:36.983984 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-11 01:18:37.046973 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-11 01:18:37.052812 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-11 01:18:37.057523 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.472   0.552  31.014

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin288.795 1.63290.444