Build/check report for BioC 3.24 - CHECK results for Maaslin2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4822
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: 1.25.1

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings Maaslin2_1.25.1.tar.gz

StartedAt: 2026-04-27 00:59:51 -0400 (Mon, 27 Apr 2026)

EndedAt: 2026-04-27 01:05:14 -0400 (Mon, 27 Apr 2026)

EllapsedTime: 322.5 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings Maaslin2_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-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: 2026-04-27 04:59:52 UTC
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.25.1’
* 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 120.504  0.993 122.153
* 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-3.24-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.25.1’
** 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"
2026-04-27 01:02:24.033602 INFO::Writing function arguments to log file
2026-04-27 01:02:24.058702 INFO::Verifying options selected are valid
2026-04-27 01:02:24.091288 INFO::Determining format of input files
2026-04-27 01:02:24.0928 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-27 01:02:24.103646 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-27 01:02:24.105167 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-27 01:02:24.107538 INFO::Filter data based on min abundance and min prevalence
2026-04-27 01:02:24.108487 INFO::Total samples in data: 1595
2026-04-27 01:02:24.109356 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-27 01:02:24.113017 INFO::Total filtered features: 0
2026-04-27 01:02:24.114124 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-27 01:02:24.120136 INFO::Total filtered features with variance filtering: 0
2026-04-27 01:02:24.121262 INFO::Filtered feature names from variance filtering:
2026-04-27 01:02:24.122137 INFO::Running selected normalization method: TSS
2026-04-27 01:02:25.161433 INFO::Bypass z-score application to metadata
2026-04-27 01:02:25.162704 INFO::Running selected transform method: AST
2026-04-27 01:02:25.180073 INFO::Running selected analysis method: LM
2026-04-27 01:02:25.780431 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-27 01:02:26.405942 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-27 01:02:26.569667 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-27 01:02:26.709603 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-27 01:02:26.853618 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-27 01:02:27.006029 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-27 01:02:27.146937 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-27 01:02:27.287291 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-27 01:02:27.402656 WARNING::Fitting problem for feature 8 a warning was issued
2026-04-27 01:02:27.545763 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-27 01:02:27.654186 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-27 01:02:27.847523 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-27 01:02:27.990343 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-27 01:02:28.130183 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-27 01:02:28.266116 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-27 01:02:28.394531 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-27 01:02:28.542671 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-27 01:02:28.686173 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-27 01:02:28.87534 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-27 01:02:29.027292 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-27 01:02:29.181202 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-27 01:02:29.326489 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-27 01:02:29.462108 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-27 01:02:29.597605 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-27 01:02:29.743982 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-27 01:02:29.886704 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-27 01:02:30.024288 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-27 01:02:30.182143 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-27 01:02:30.333719 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-27 01:02:30.479122 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-27 01:02:30.642932 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-27 01:02:30.790115 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-27 01:02:30.944824 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-27 01:02:31.088074 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-27 01:02:31.233518 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-27 01:02:31.383902 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-27 01:02:31.526449 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-27 01:02:31.668376 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-27 01:02:31.810051 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-27 01:02:31.954001 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-27 01:02:32.114669 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-27 01:02:32.260272 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-27 01:02:32.421767 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-27 01:02:32.564844 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-27 01:02:32.708567 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-27 01:02:32.851111 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-27 01:02:32.99674 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-27 01:02:33.134044 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-27 01:02:33.275859 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-27 01:02:33.418069 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-27 01:02:33.573261 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-27 01:02:33.712592 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-27 01:02:33.859409 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-27 01:02:34.010143 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-27 01:02:34.155859 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-27 01:02:34.304207 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-27 01:02:34.454941 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-27 01:02:34.587892 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-27 01:02:34.761738 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-27 01:02:34.91224 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-27 01:02:35.051131 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-27 01:02:35.203123 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-27 01:02:35.346208 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-27 01:02:35.481581 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-27 01:02:35.88648 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-27 01:02:36.026113 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-27 01:02:36.160923 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-27 01:02:36.29921 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-27 01:02:36.441607 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-27 01:02:36.580922 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-27 01:02:36.710643 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-27 01:02:36.860599 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-27 01:02:37.01052 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-27 01:02:37.157943 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-27 01:02:37.297598 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-27 01:02:37.465559 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-27 01:02:37.604428 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-27 01:02:37.751573 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-27 01:02:37.915269 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-27 01:02:38.056749 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-27 01:02:38.203417 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-27 01:02:38.350801 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-27 01:02:38.503272 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-27 01:02:38.644933 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-27 01:02:38.793581 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-27 01:02:38.938073 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-27 01:02:39.09726 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-27 01:02:39.240339 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-27 01:02:39.380404 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-27 01:02:39.530522 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-27 01:02:39.712672 INFO::Counting total values for each feature
2026-04-27 01:02:39.742437 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-27 01:02:39.842493 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-27 01:02:39.94103 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-27 01:02:40.042892 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-27 01:02:40.091659 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-27 01:02:40.119014 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-27 01:02:40.124465 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-27 01:02:40.129805 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"
2026-04-27 01:02:40.144413 INFO::Writing function arguments to log file
2026-04-27 01:02:40.150793 INFO::Verifying options selected are valid
2026-04-27 01:02:40.151882 INFO::Determining format of input files
2026-04-27 01:02:40.153199 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-27 01:02:40.159012 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-27 01:02:40.16024 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-04-27 01:02:40.162033 INFO::Filter data based on min abundance and min prevalence
2026-04-27 01:02:40.162979 INFO::Total samples in data: 1595
2026-04-27 01:02:40.163888 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-27 01:02:40.168363 INFO::Total filtered features: 0
2026-04-27 01:02:40.169516 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-27 01:02:40.189852 INFO::Total filtered features with variance filtering: 0
2026-04-27 01:02:40.191211 INFO::Filtered feature names from variance filtering:
2026-04-27 01:02:40.192151 INFO::Running selected normalization method: NONE
2026-04-27 01:02:40.193053 INFO::Bypass z-score application to metadata
2026-04-27 01:02:40.193985 INFO::Running selected transform method: AST
2026-04-27 01:02:40.209404 INFO::Running selected analysis method: LM
2026-04-27 01:02:40.21124 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-27 01:02:40.351924 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-27 01:02:40.493894 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-27 01:02:40.629096 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-27 01:02:40.758275 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-27 01:02:40.888828 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-27 01:02:41.032881 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-27 01:02:41.164345 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-27 01:02:41.291207 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-27 01:02:41.42346 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-27 01:02:41.566154 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-27 01:02:41.675993 WARNING::Fitting problem for feature 11 a warning was issued
2026-04-27 01:02:41.815316 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-27 01:02:41.94224 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-27 01:02:42.076643 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-27 01:02:42.204661 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-27 01:02:42.340719 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-27 01:02:42.449888 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-27 01:02:42.5808 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-27 01:02:42.718389 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-27 01:02:42.855106 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-27 01:02:42.979305 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-27 01:02:43.110859 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-27 01:02:43.250701 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-27 01:02:43.386205 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-27 01:02:43.515407 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-27 01:02:43.656462 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-27 01:02:43.784587 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-27 01:02:43.912013 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-27 01:02:44.052435 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-27 01:02:44.179672 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-27 01:02:44.302715 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-27 01:02:44.440724 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-27 01:02:44.572482 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-27 01:02:44.70334 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-27 01:02:44.834214 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-27 01:02:44.965352 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-27 01:02:45.099017 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-27 01:02:45.230882 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-27 01:02:45.366811 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-27 01:02:45.526964 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-27 01:02:45.656041 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-27 01:02:45.78611 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-27 01:02:45.930092 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-27 01:02:46.059117 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-27 01:02:46.198833 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-27 01:02:46.342683 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-27 01:02:46.490436 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-27 01:02:46.625791 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-27 01:02:46.754996 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-27 01:02:46.893679 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-27 01:02:47.035555 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-27 01:02:47.159086 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-27 01:02:47.29799 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-27 01:02:47.427171 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-27 01:02:47.563754 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-27 01:02:47.694324 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-27 01:02:47.826288 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-27 01:02:47.968139 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-27 01:02:48.099491 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-27 01:02:48.227793 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-27 01:02:48.360403 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-27 01:02:48.500301 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-27 01:02:48.633844 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-27 01:02:48.782799 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-27 01:02:48.922798 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-27 01:02:49.075351 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-27 01:02:49.211392 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-27 01:02:49.343466 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-27 01:02:49.453101 WARNING::Fitting problem for feature 67 a warning was issued
2026-04-27 01:02:49.599174 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-27 01:02:49.72736 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-27 01:02:49.868366 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-27 01:02:50.01903 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-27 01:02:50.153133 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-27 01:02:50.2003 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-27 01:02:50.33441 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-27 01:02:50.473353 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-27 01:02:50.603639 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-27 01:02:50.734892 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-27 01:02:50.868396 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-27 01:02:51.008684 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-27 01:02:51.146578 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-27 01:02:51.287809 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-27 01:02:51.438058 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-27 01:02:51.580535 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-27 01:02:51.710506 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-27 01:02:51.86744 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-27 01:02:51.998791 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-27 01:02:52.132212 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-27 01:02:52.276473 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-27 01:02:52.43524 INFO::Counting total values for each feature
2026-04-27 01:02:52.457467 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-27 01:02:52.55337 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-27 01:02:52.649516 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-27 01:02:52.756526 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-27 01:02:52.820826 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-27 01:02:52.88284 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-27 01:02:52.888337 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-27 01:02:52.892761 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 
 29.430   0.577  29.998

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	120.504	0.993	122.153