Back to Multiple platform build/check report for BioC 3.23:   simplified   long
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This page was generated on 2026-04-30 11:35 -0400 (Thu, 30 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4988
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-04-24 r89963) -- "Because it was There" 4718
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 1199/2418HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.26.0  (landing page)
Sagun Maharjan
Snapshot Date: 2026-04-29 13:40 -0400 (Wed, 29 Apr 2026)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_23
git_last_commit: 0616fc9
git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026)
nebbiolo1Linux (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    OK  UNNEEDED, same version is already published
See other builds for Maaslin2 in R Universe.

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: 1.26.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Maaslin2_1.26.0.tar.gz
StartedAt: 2026-04-30 01:39:35 -0400 (Thu, 30 Apr 2026)
EndedAt: 2026-04-30 01:45:07 -0400 (Thu, 30 Apr 2026)
EllapsedTime: 331.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Maaslin2_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 05:39:36 UTC
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.26.0’
* 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: 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 124.595  1.609 128.929
* 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-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.26.0’
** 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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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"
2026-04-30 01:42:14.953412 INFO::Writing function arguments to log file
2026-04-30 01:42:14.980226 INFO::Verifying options selected are valid
2026-04-30 01:42:15.016523 INFO::Determining format of input files
2026-04-30 01:42:15.018301 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-30 01:42:15.031409 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-30 01:42:15.033049 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-30 01:42:15.035551 INFO::Filter data based on min abundance and min prevalence
2026-04-30 01:42:15.036572 INFO::Total samples in data: 1595
2026-04-30 01:42:15.037471 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-30 01:42:15.041513 INFO::Total filtered features: 0
2026-04-30 01:42:15.042595 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-30 01:42:15.049002 INFO::Total filtered features with variance filtering: 0
2026-04-30 01:42:15.050213 INFO::Filtered feature names from variance filtering:
2026-04-30 01:42:15.05115 INFO::Running selected normalization method: TSS
2026-04-30 01:42:16.136416 INFO::Bypass z-score application to metadata
2026-04-30 01:42:16.137747 INFO::Running selected transform method: AST
2026-04-30 01:42:16.154712 INFO::Running selected analysis method: LM
2026-04-30 01:42:16.78105 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-30 01:42:17.393336 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-30 01:42:17.562562 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-30 01:42:17.704219 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-30 01:42:17.847232 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-30 01:42:18.000383 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-30 01:42:18.140016 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-30 01:42:18.281095 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-30 01:42:18.39616 WARNING::Fitting problem for feature 8 a warning was issued
2026-04-30 01:42:18.544374 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-30 01:42:18.655909 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-30 01:42:18.859105 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-30 01:42:19.00031 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-30 01:42:19.156376 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-30 01:42:19.298312 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-30 01:42:19.424886 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-30 01:42:19.576089 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-30 01:42:19.717951 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-30 01:42:19.868045 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-30 01:42:20.022179 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-30 01:42:20.179648 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-30 01:42:20.350133 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-30 01:42:20.496258 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-30 01:42:20.631456 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-30 01:42:20.775738 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-30 01:42:20.920387 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-30 01:42:21.059597 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-30 01:42:21.208747 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-30 01:42:21.349796 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-30 01:42:21.485707 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-30 01:42:21.636531 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-30 01:42:21.777432 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-30 01:42:21.926588 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-30 01:42:22.064529 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-30 01:42:22.216085 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-30 01:42:22.373875 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-30 01:42:22.521124 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-30 01:42:22.663939 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-30 01:42:22.808162 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-30 01:42:22.955711 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-30 01:42:23.104052 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-30 01:42:23.253133 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-30 01:42:23.401339 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-30 01:42:23.54765 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-30 01:42:23.693139 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-30 01:42:23.839779 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-30 01:42:23.988097 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-30 01:42:24.126014 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-30 01:42:24.271801 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-30 01:42:24.418002 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-30 01:42:24.571589 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-30 01:42:24.713095 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-30 01:42:24.857731 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-30 01:42:25.011722 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-30 01:42:25.169016 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-30 01:42:25.326393 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-30 01:42:25.488155 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-30 01:42:25.626314 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-30 01:42:25.81101 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-30 01:42:25.969146 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-30 01:42:26.116786 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-30 01:42:26.273384 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-30 01:42:26.41454 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-30 01:42:26.554343 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-30 01:42:26.981769 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-30 01:42:27.125341 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-30 01:42:27.265881 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-30 01:42:27.404299 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-30 01:42:27.54514 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-30 01:42:27.6839 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-30 01:42:27.820843 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-30 01:42:27.981863 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-30 01:42:28.134694 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-30 01:42:28.282444 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-30 01:42:28.422503 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-30 01:42:28.570337 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-30 01:42:28.709167 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-30 01:42:28.84804 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-30 01:42:28.9951 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-30 01:42:29.136077 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-30 01:42:29.283954 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-30 01:42:29.435035 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-30 01:42:29.589616 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-30 01:42:29.730937 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-30 01:42:29.875311 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-30 01:42:30.014156 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-30 01:42:30.153833 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-30 01:42:30.295561 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-30 01:42:30.432697 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-30 01:42:30.580338 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-30 01:42:30.761528 INFO::Counting total values for each feature
2026-04-30 01:42:30.791299 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-30 01:42:30.885842 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-30 01:42:30.982808 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-30 01:42:31.081907 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-30 01:42:31.130926 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-30 01:42:31.158511 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-30 01:42:31.164062 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-30 01:42:31.16934 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"
2026-04-30 01:42:31.182325 INFO::Writing function arguments to log file
2026-04-30 01:42:31.188434 INFO::Verifying options selected are valid
2026-04-30 01:42:31.189442 INFO::Determining format of input files
2026-04-30 01:42:31.190665 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-30 01:42:31.195748 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-30 01:42:31.196874 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-04-30 01:42:31.198537 INFO::Filter data based on min abundance and min prevalence
2026-04-30 01:42:31.199448 INFO::Total samples in data: 1595
2026-04-30 01:42:31.200356 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-30 01:42:31.204125 INFO::Total filtered features: 0
2026-04-30 01:42:31.205147 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-30 01:42:31.218664 INFO::Total filtered features with variance filtering: 0
2026-04-30 01:42:31.21988 INFO::Filtered feature names from variance filtering:
2026-04-30 01:42:31.220756 INFO::Running selected normalization method: NONE
2026-04-30 01:42:31.221622 INFO::Bypass z-score application to metadata
2026-04-30 01:42:31.222474 INFO::Running selected transform method: AST
2026-04-30 01:42:31.236952 INFO::Running selected analysis method: LM
2026-04-30 01:42:31.238646 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-30 01:42:31.36989 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-30 01:42:31.504751 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-30 01:42:31.635273 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-30 01:42:31.765748 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-30 01:42:31.899119 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-30 01:42:32.04184 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-30 01:42:32.177891 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-30 01:42:32.312068 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-30 01:42:32.454555 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-30 01:42:32.607707 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-30 01:42:32.723212 WARNING::Fitting problem for feature 11 a warning was issued
2026-04-30 01:42:32.862273 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-30 01:42:33.003315 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-30 01:42:33.158806 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-30 01:42:33.290657 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-30 01:42:33.438824 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-30 01:42:33.554219 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-30 01:42:33.688048 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-30 01:42:33.827546 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-30 01:42:33.96611 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-30 01:42:34.094149 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-30 01:42:34.227714 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-30 01:42:34.370443 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-30 01:42:34.506412 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-30 01:42:34.634199 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-30 01:42:34.775529 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-30 01:42:34.903936 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-30 01:42:35.033662 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-30 01:42:35.174935 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-30 01:42:35.30226 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-30 01:42:35.426768 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-30 01:42:35.564126 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-30 01:42:35.696839 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-30 01:42:35.829358 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-30 01:42:35.964997 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-30 01:42:36.097832 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-30 01:42:36.236172 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-30 01:42:36.370296 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-30 01:42:36.507716 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-30 01:42:36.676206 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-30 01:42:36.806055 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-30 01:42:36.939605 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-30 01:42:37.085582 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-30 01:42:37.270752 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-30 01:42:37.411002 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-30 01:42:37.554419 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-30 01:42:37.710069 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-30 01:42:37.855076 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-30 01:42:37.997353 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-30 01:42:38.149548 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-30 01:42:38.304958 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-30 01:42:38.431943 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-30 01:42:38.566025 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-30 01:42:38.687937 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-30 01:42:38.822993 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-30 01:42:38.946626 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-30 01:42:39.07789 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-30 01:42:39.219983 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-30 01:42:39.350821 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-30 01:42:39.479941 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-30 01:42:39.619097 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-30 01:42:39.75564 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-30 01:42:39.886328 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-30 01:42:40.015767 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-30 01:42:40.148568 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-30 01:42:40.295912 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-30 01:42:40.426563 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-30 01:42:40.562546 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-30 01:42:40.675625 WARNING::Fitting problem for feature 67 a warning was issued
2026-04-30 01:42:40.831462 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-30 01:42:40.962864 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-30 01:42:41.103555 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-30 01:42:41.256124 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-30 01:42:41.388098 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-30 01:42:41.435341 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-30 01:42:41.571761 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-30 01:42:41.713336 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-30 01:42:41.846271 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-30 01:42:41.979473 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-30 01:42:42.120633 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-30 01:42:42.260916 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-30 01:42:42.398431 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-30 01:42:42.534456 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-30 01:42:42.676577 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-30 01:42:42.818424 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-30 01:42:42.949201 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-30 01:42:43.094107 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-30 01:42:43.228707 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-30 01:42:43.363894 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-30 01:42:43.511096 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-30 01:42:43.6806 INFO::Counting total values for each feature
2026-04-30 01:42:43.704382 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-30 01:42:43.79943 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-30 01:42:43.893928 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-30 01:42:43.999368 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-30 01:42:44.06425 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-30 01:42:44.127201 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-30 01:42:44.132843 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-30 01:42:44.137539 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 
 29.821   0.564  30.379

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2124.595 1.609128.929