Build/check report for BioC 3.22 - CHECK results for Maaslin2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4897
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*

CHECK results for Maaslin2 on nebbiolo2

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: 1.24.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.24.1.tar.gz

StartedAt: 2026-04-04 00:50:48 -0400 (Sat, 04 Apr 2026)

EndedAt: 2026-04-04 00:56:16 -0400 (Sat, 04 Apr 2026)

EllapsedTime: 328.4 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.24.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 123.234  1.251 126.882
* 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-3.22-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.24.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.19
Current TMB package version is 1.9.21
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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"
2026-04-04 00:53:24.759791 INFO::Writing function arguments to log file
2026-04-04 00:53:24.801501 INFO::Verifying options selected are valid
2026-04-04 00:53:24.83871 INFO::Determining format of input files
2026-04-04 00:53:24.840386 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-04 00:53:24.845964 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-04 00:53:24.847366 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-04 00:53:24.849851 INFO::Filter data based on min abundance and min prevalence
2026-04-04 00:53:24.850771 INFO::Total samples in data: 1595
2026-04-04 00:53:24.851677 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-04 00:53:24.855884 INFO::Total filtered features: 0
2026-04-04 00:53:24.857005 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-04 00:53:24.8719 INFO::Total filtered features with variance filtering: 0
2026-04-04 00:53:24.873171 INFO::Filtered feature names from variance filtering:
2026-04-04 00:53:24.874089 INFO::Running selected normalization method: TSS
2026-04-04 00:53:25.908826 INFO::Bypass z-score application to metadata
2026-04-04 00:53:25.910126 INFO::Running selected transform method: AST
2026-04-04 00:53:25.927617 INFO::Running selected analysis method: LM
2026-04-04 00:53:26.561689 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-04 00:53:27.168542 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-04 00:53:27.339532 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-04 00:53:27.485362 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-04 00:53:27.63219 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-04 00:53:27.786497 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-04 00:53:27.927123 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-04 00:53:28.07351 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-04 00:53:28.192875 WARNING::Fitting problem for feature 8 a warning was issued
2026-04-04 00:53:28.34219 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-04 00:53:28.454469 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-04 00:53:28.656008 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-04 00:53:28.79704 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-04 00:53:28.940989 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-04 00:53:29.363014 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-04 00:53:29.476413 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-04 00:53:29.62258 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-04 00:53:29.769357 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-04 00:53:29.94557 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-04 00:53:30.091748 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-04 00:53:30.24946 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-04 00:53:30.410012 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-04 00:53:30.539953 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-04 00:53:30.674102 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-04 00:53:30.814532 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-04 00:53:30.963709 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-04 00:53:31.102836 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-04 00:53:31.250221 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-04 00:53:31.400637 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-04 00:53:31.534961 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-04 00:53:31.679855 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-04 00:53:31.823995 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-04 00:53:31.977499 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-04 00:53:32.11771 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-04 00:53:32.275083 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-04 00:53:32.441332 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-04 00:53:32.595802 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-04 00:53:32.741366 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-04 00:53:32.891333 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-04 00:53:33.041186 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-04 00:53:33.184209 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-04 00:53:33.317236 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-04 00:53:33.453162 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-04 00:53:33.599478 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-04 00:53:33.735232 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-04 00:53:33.877423 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-04 00:53:34.025027 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-04 00:53:34.15918 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-04 00:53:34.298775 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-04 00:53:34.442841 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-04 00:53:34.596949 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-04 00:53:34.734028 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-04 00:53:34.892481 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-04 00:53:35.049147 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-04 00:53:35.196982 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-04 00:53:35.350306 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-04 00:53:35.497575 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-04 00:53:35.638075 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-04 00:53:35.784701 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-04 00:53:35.941581 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-04 00:53:36.087979 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-04 00:53:36.228512 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-04 00:53:36.366802 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-04 00:53:36.506618 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-04 00:53:36.66986 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-04 00:53:36.81577 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-04 00:53:36.963885 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-04 00:53:37.110764 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-04 00:53:37.24803 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-04 00:53:37.39292 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-04 00:53:37.533122 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-04 00:53:37.684551 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-04 00:53:37.840562 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-04 00:53:38.00654 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-04 00:53:38.146864 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-04 00:53:38.293891 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-04 00:53:38.450615 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-04 00:53:38.587738 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-04 00:53:38.729819 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-04 00:53:38.874499 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-04 00:53:39.015907 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-04 00:53:39.167039 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-04 00:53:39.32051 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-04 00:53:39.462378 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-04 00:53:39.625968 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-04 00:53:39.768109 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-04 00:53:39.906389 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-04 00:53:40.050923 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-04 00:53:40.197831 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-04 00:53:40.341333 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-04 00:53:40.546891 INFO::Counting total values for each feature
2026-04-04 00:53:40.580246 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-04 00:53:40.674137 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-04 00:53:40.769568 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-04 00:53:40.866691 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-04 00:53:40.914618 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-04 00:53:40.941223 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-04 00:53:40.94652 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-04 00:53:40.951593 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"
2026-04-04 00:53:40.964595 INFO::Writing function arguments to log file
2026-04-04 00:53:40.970055 INFO::Verifying options selected are valid
2026-04-04 00:53:40.971072 INFO::Determining format of input files
2026-04-04 00:53:40.972257 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-04 00:53:40.97732 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-04 00:53:40.978371 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-04-04 00:53:40.979922 INFO::Filter data based on min abundance and min prevalence
2026-04-04 00:53:40.980765 INFO::Total samples in data: 1595
2026-04-04 00:53:40.981587 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-04 00:53:40.985198 INFO::Total filtered features: 0
2026-04-04 00:53:40.986139 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-04 00:53:40.993155 INFO::Total filtered features with variance filtering: 0
2026-04-04 00:53:40.994239 INFO::Filtered feature names from variance filtering:
2026-04-04 00:53:40.995065 INFO::Running selected normalization method: NONE
2026-04-04 00:53:40.995864 INFO::Bypass z-score application to metadata
2026-04-04 00:53:40.996669 INFO::Running selected transform method: AST
2026-04-04 00:53:41.011518 INFO::Running selected analysis method: LM
2026-04-04 00:53:41.013135 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-04 00:53:41.155383 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-04 00:53:41.292027 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-04 00:53:41.419871 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-04 00:53:41.555939 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-04 00:53:41.698488 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-04 00:53:41.837698 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-04 00:53:41.979445 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-04 00:53:42.125503 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-04 00:53:42.265436 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-04 00:53:42.408789 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-04 00:53:42.527552 WARNING::Fitting problem for feature 11 a warning was issued
2026-04-04 00:53:42.681032 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-04 00:53:42.810321 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-04 00:53:42.962684 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-04 00:53:43.10108 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-04 00:53:43.259478 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-04 00:53:43.370682 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-04 00:53:43.507177 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-04 00:53:43.655411 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-04 00:53:43.788379 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-04 00:53:43.915933 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-04 00:53:44.051236 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-04 00:53:44.192791 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-04 00:53:44.3295 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-04 00:53:44.464395 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-04 00:53:44.61316 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-04 00:53:44.746438 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-04 00:53:44.880785 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-04 00:53:45.032068 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-04 00:53:45.16203 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-04 00:53:45.288771 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-04 00:53:45.432318 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-04 00:53:45.570517 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-04 00:53:45.703784 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-04 00:53:45.841097 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-04 00:53:45.976301 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-04 00:53:46.108613 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-04 00:53:46.253811 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-04 00:53:46.392979 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-04 00:53:46.554255 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-04 00:53:46.685957 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-04 00:53:46.815442 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-04 00:53:46.953173 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-04 00:53:47.080459 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-04 00:53:47.225026 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-04 00:53:47.361748 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-04 00:53:47.494757 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-04 00:53:47.63684 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-04 00:53:47.766317 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-04 00:53:47.911405 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-04 00:53:48.042634 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-04 00:53:48.171832 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-04 00:53:48.305443 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-04 00:53:48.684841 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-04 00:53:48.804743 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-04 00:53:48.9311 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-04 00:53:49.066049 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-04 00:53:49.209122 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-04 00:53:49.341251 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-04 00:53:49.470341 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-04 00:53:49.603367 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-04 00:53:49.735083 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-04 00:53:49.867458 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-04 00:53:49.997452 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-04 00:53:50.133925 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-04 00:53:50.264009 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-04 00:53:50.392329 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-04 00:53:50.524295 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-04 00:53:50.639672 WARNING::Fitting problem for feature 67 a warning was issued
2026-04-04 00:53:50.776317 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-04 00:53:50.90662 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-04 00:53:51.045674 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-04 00:53:51.194308 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-04 00:53:51.327672 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-04 00:53:51.376072 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-04 00:53:51.514132 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-04 00:53:51.654908 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-04 00:53:51.787737 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-04 00:53:51.922049 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-04 00:53:52.056986 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-04 00:53:52.197621 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-04 00:53:52.333187 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-04 00:53:52.472035 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-04 00:53:52.610359 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-04 00:53:52.750628 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-04 00:53:52.883462 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-04 00:53:53.013441 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-04 00:53:53.146637 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-04 00:53:53.275909 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-04 00:53:53.412751 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-04 00:53:53.580717 INFO::Counting total values for each feature
2026-04-04 00:53:53.602422 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-04 00:53:53.695099 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-04 00:53:53.789653 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-04 00:53:53.887675 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-04 00:53:53.951378 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-04 00:53:54.01316 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-04 00:53:54.01857 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-04 00:53:54.022944 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 
 29.865   0.525  30.380

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	123.234	1.251	126.882