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"	4896
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: 2026-04-01 00:54:53 -0400 (Wed, 01 Apr 2026)

EndedAt: 2026-04-01 01:00:17 -0400 (Wed, 01 Apr 2026)

EllapsedTime: 323.5 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 121.422  1.106 123.925
* 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"
2026-04-01 00:57:27.713257 INFO::Writing function arguments to log file
2026-04-01 00:57:27.754199 INFO::Verifying options selected are valid
2026-04-01 00:57:27.787633 INFO::Determining format of input files
2026-04-01 00:57:27.789231 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-01 00:57:27.794351 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-01 00:57:27.795618 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-01 00:57:27.797945 INFO::Filter data based on min abundance and min prevalence
2026-04-01 00:57:27.798807 INFO::Total samples in data: 1595
2026-04-01 00:57:27.799644 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-01 00:57:27.803358 INFO::Total filtered features: 0
2026-04-01 00:57:27.804371 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-01 00:57:27.817528 INFO::Total filtered features with variance filtering: 0
2026-04-01 00:57:27.818641 INFO::Filtered feature names from variance filtering:
2026-04-01 00:57:27.819467 INFO::Running selected normalization method: TSS
2026-04-01 00:57:28.894145 INFO::Bypass z-score application to metadata
2026-04-01 00:57:28.895559 INFO::Running selected transform method: AST
2026-04-01 00:57:28.913222 INFO::Running selected analysis method: LM
2026-04-01 00:57:29.571188 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-01 00:57:30.189329 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-01 00:57:30.368518 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-01 00:57:30.519504 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-01 00:57:30.675863 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-01 00:57:30.837999 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-01 00:57:30.978358 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-01 00:57:31.120483 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-01 00:57:31.24035 WARNING::Fitting problem for feature 8 a warning was issued
2026-04-01 00:57:31.386999 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-01 00:57:31.497475 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-01 00:57:31.697647 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-01 00:57:31.839093 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-01 00:57:31.982013 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-01 00:57:32.359435 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-01 00:57:32.473165 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-01 00:57:32.621394 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-01 00:57:32.768573 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-01 00:57:32.939621 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-01 00:57:33.084295 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-01 00:57:33.240628 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-01 00:57:33.403651 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-01 00:57:33.537309 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-01 00:57:33.674418 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-01 00:57:33.820081 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-01 00:57:33.974769 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-01 00:57:34.113576 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-01 00:57:34.263816 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-01 00:57:34.410326 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-01 00:57:34.545811 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-01 00:57:34.698766 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-01 00:57:34.847531 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-01 00:57:34.99726 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-01 00:57:35.140229 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-01 00:57:35.295469 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-01 00:57:35.452721 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-01 00:57:35.598442 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-01 00:57:35.731707 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-01 00:57:35.871557 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-01 00:57:36.017748 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-01 00:57:36.157573 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-01 00:57:36.291199 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-01 00:57:36.432518 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-01 00:57:36.583362 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-01 00:57:36.726107 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-01 00:57:36.875484 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-01 00:57:37.028166 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-01 00:57:37.167578 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-01 00:57:37.319167 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-01 00:57:37.466584 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-01 00:57:37.619664 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-01 00:57:37.760919 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-01 00:57:37.917315 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-01 00:57:38.075218 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-01 00:57:38.220924 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-01 00:57:38.367267 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-01 00:57:38.51632 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-01 00:57:38.657567 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-01 00:57:38.804862 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-01 00:57:38.960803 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-01 00:57:39.107693 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-01 00:57:39.248665 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-01 00:57:39.390368 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-01 00:57:39.524574 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-01 00:57:39.670411 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-01 00:57:39.809262 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-01 00:57:39.946116 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-01 00:57:40.086959 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-01 00:57:40.221654 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-01 00:57:40.36191 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-01 00:57:40.496663 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-01 00:57:40.644385 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-01 00:57:40.797925 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-01 00:57:40.964551 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-01 00:57:41.101714 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-01 00:57:41.243574 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-01 00:57:41.384848 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-01 00:57:41.518901 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-01 00:57:41.659351 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-01 00:57:41.806308 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-01 00:57:41.947638 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-01 00:57:42.096872 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-01 00:57:42.249118 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-01 00:57:42.392215 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-01 00:57:42.558609 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-01 00:57:42.697153 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-01 00:57:42.835394 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-01 00:57:42.982126 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-01 00:57:43.124742 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-01 00:57:43.260314 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-01 00:57:43.450772 INFO::Counting total values for each feature
2026-04-01 00:57:43.482994 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-01 00:57:43.576167 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-01 00:57:43.671466 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-01 00:57:43.768107 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-01 00:57:43.816018 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-01 00:57:43.842736 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-01 00:57:43.848039 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-01 00:57:43.853095 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"
2026-04-01 00:57:43.866368 INFO::Writing function arguments to log file
2026-04-01 00:57:43.871932 INFO::Verifying options selected are valid
2026-04-01 00:57:43.872921 INFO::Determining format of input files
2026-04-01 00:57:43.874115 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-01 00:57:43.879185 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-01 00:57:43.880231 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-04-01 00:57:43.881791 INFO::Filter data based on min abundance and min prevalence
2026-04-01 00:57:43.882627 INFO::Total samples in data: 1595
2026-04-01 00:57:43.883441 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-01 00:57:43.887103 INFO::Total filtered features: 0
2026-04-01 00:57:43.888053 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-01 00:57:43.895085 INFO::Total filtered features with variance filtering: 0
2026-04-01 00:57:43.896121 INFO::Filtered feature names from variance filtering:
2026-04-01 00:57:43.896942 INFO::Running selected normalization method: NONE
2026-04-01 00:57:43.89773 INFO::Bypass z-score application to metadata
2026-04-01 00:57:43.898524 INFO::Running selected transform method: AST
2026-04-01 00:57:43.912942 INFO::Running selected analysis method: LM
2026-04-01 00:57:43.914497 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-01 00:57:44.052895 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-01 00:57:44.186986 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-01 00:57:44.318714 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-01 00:57:44.452127 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-01 00:57:44.590808 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-01 00:57:44.724648 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-01 00:57:44.861746 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-01 00:57:45.004714 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-01 00:57:45.142284 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-01 00:57:45.281013 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-01 00:57:45.397339 WARNING::Fitting problem for feature 11 a warning was issued
2026-04-01 00:57:45.549848 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-01 00:57:45.677129 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-01 00:57:45.80938 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-01 00:57:45.96002 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-01 00:57:46.119712 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-01 00:57:46.228791 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-01 00:57:46.373389 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-01 00:57:46.522949 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-01 00:57:46.654993 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-01 00:57:46.783443 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-01 00:57:46.924968 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-01 00:57:47.072857 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-01 00:57:47.209948 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-01 00:57:47.341402 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-01 00:57:47.489643 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-01 00:57:47.620232 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-01 00:57:47.751643 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-01 00:57:47.902384 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-01 00:57:48.034023 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-01 00:57:48.162489 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-01 00:57:48.303039 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-01 00:57:48.436001 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-01 00:57:48.570472 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-01 00:57:48.704352 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-01 00:57:48.836502 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-01 00:57:48.967267 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-01 00:57:49.109602 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-01 00:57:49.24702 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-01 00:57:49.393031 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-01 00:57:49.534639 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-01 00:57:49.66385 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-01 00:57:49.808387 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-01 00:57:49.941586 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-01 00:57:50.090735 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-01 00:57:50.234182 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-01 00:57:50.368194 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-01 00:57:50.511305 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-01 00:57:50.639552 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-01 00:57:50.781907 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-01 00:57:50.912153 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-01 00:57:51.041968 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-01 00:57:51.172802 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-01 00:57:51.563682 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-01 00:57:51.687896 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-01 00:57:51.818373 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-01 00:57:51.954454 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-01 00:57:52.095127 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-01 00:57:52.225996 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-01 00:57:52.353982 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-01 00:57:52.487297 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-01 00:57:52.621091 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-01 00:57:52.751662 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-01 00:57:52.880008 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-01 00:57:53.019828 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-01 00:57:53.149942 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-01 00:57:53.27799 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-01 00:57:53.408818 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-01 00:57:53.524981 WARNING::Fitting problem for feature 67 a warning was issued
2026-04-01 00:57:53.662567 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-01 00:57:53.791295 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-01 00:57:53.92932 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-01 00:57:54.078081 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-01 00:57:54.211493 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-01 00:57:54.25977 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-01 00:57:54.39603 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-01 00:57:54.536666 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-01 00:57:54.669092 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-01 00:57:54.800826 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-01 00:57:54.932868 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-01 00:57:55.071035 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-01 00:57:55.206601 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-01 00:57:55.34116 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-01 00:57:55.476167 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-01 00:57:55.613906 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-01 00:57:55.740258 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-01 00:57:55.872357 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-01 00:57:56.007484 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-01 00:57:56.136053 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-01 00:57:56.272992 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-01 00:57:56.445463 INFO::Counting total values for each feature
2026-04-01 00:57:56.467429 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-01 00:57:56.55989 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-01 00:57:56.652809 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-01 00:57:56.750174 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-01 00:57:56.813866 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-01 00:57:56.875763 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-01 00:57:56.881202 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-01 00:57:56.885433 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 
 29.737   0.555  30.285

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	121.422	1.106	123.925