Multiple platform build/check report for BioC 3.23 - CHECK results for Maaslin2 on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.6.0 alpha (2026-03-30 r89742)	4816
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-03-28 r89739)	4539
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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.25.1.tar.gz

StartedAt: 2026-03-31 20:03:52 -0400 (Tue, 31 Mar 2026)

EndedAt: 2026-03-31 20:05:06 -0400 (Tue, 31 Mar 2026)

EllapsedTime: 73.9 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-01 00:03:52 UTC
* using option ‘--no-vignettes’
* 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 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 40.986  0.726   42.21
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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"
2026-03-31 20:04:50.809113 INFO::Writing function arguments to log file
2026-03-31 20:04:50.827602 INFO::Verifying options selected are valid
2026-03-31 20:04:50.841625 INFO::Determining format of input files
2026-03-31 20:04:50.842548 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 20:04:50.8452 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-31 20:04:50.845818 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-03-31 20:04:50.846743 INFO::Filter data based on min abundance and min prevalence
2026-03-31 20:04:50.847198 INFO::Total samples in data: 1595
2026-03-31 20:04:50.847604 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-31 20:04:50.849428 INFO::Total filtered features: 0
2026-03-31 20:04:50.84999 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-31 20:04:50.853134 INFO::Total filtered features with variance filtering: 0
2026-03-31 20:04:50.853668 INFO::Filtered feature names from variance filtering:
2026-03-31 20:04:50.854063 INFO::Running selected normalization method: TSS
2026-03-31 20:04:51.267372 INFO::Bypass z-score application to metadata
2026-03-31 20:04:51.268329 INFO::Running selected transform method: AST
2026-03-31 20:04:51.276249 INFO::Running selected analysis method: LM
2026-03-31 20:04:51.571455 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-31 20:04:51.811166 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-31 20:04:51.872252 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-31 20:04:51.926081 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-31 20:04:51.989012 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-31 20:04:52.046454 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-31 20:04:52.110475 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-31 20:04:52.171309 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-31 20:04:52.226354 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-31 20:04:52.298129 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-31 20:04:52.361152 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-31 20:04:52.413471 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-31 20:04:52.497517 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-31 20:04:52.541394 WARNING::Fitting problem for feature 13 a warning was issued
2026-03-31 20:04:52.598287 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-31 20:04:52.661288 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-31 20:04:52.719822 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-31 20:04:52.772503 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-31 20:04:52.844263 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-31 20:04:52.90021 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-31 20:04:52.947839 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-31 20:04:53.002023 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-31 20:04:53.071859 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-31 20:04:53.125655 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-31 20:04:53.187576 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-31 20:04:53.353935 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-31 20:04:53.409208 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-31 20:04:53.46007 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-31 20:04:53.517716 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-31 20:04:53.57534 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-31 20:04:53.62943 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-31 20:04:53.683598 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-31 20:04:53.747317 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-31 20:04:53.80372 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-31 20:04:53.859453 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-31 20:04:53.919599 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-31 20:04:53.982598 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-31 20:04:54.043824 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-31 20:04:54.096786 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-31 20:04:54.144441 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-31 20:04:54.194171 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-31 20:04:54.250226 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-31 20:04:54.299264 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-31 20:04:54.351353 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-31 20:04:54.402909 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-31 20:04:54.462929 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-31 20:04:54.513734 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-31 20:04:54.565373 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-31 20:04:54.619689 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-31 20:04:54.673569 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-31 20:04:54.724752 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-31 20:04:54.777099 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-31 20:04:54.831525 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-31 20:04:54.88493 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-31 20:04:54.936846 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-31 20:04:54.984091 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-31 20:04:55.037355 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-31 20:04:55.097442 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-31 20:04:55.146037 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-31 20:04:55.19753 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-31 20:04:55.248182 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-31 20:04:55.299769 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-31 20:04:55.351778 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-31 20:04:55.404344 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-31 20:04:55.458671 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-31 20:04:55.514282 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-31 20:04:55.563757 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-31 20:04:55.615437 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-31 20:04:55.668395 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-31 20:04:55.722471 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-31 20:04:55.777497 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-31 20:04:55.831614 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-31 20:04:55.884741 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-31 20:04:55.935099 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-31 20:04:55.983954 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-31 20:04:56.035561 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-31 20:04:56.091313 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-31 20:04:56.142357 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-31 20:04:56.193755 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-31 20:04:56.251575 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-31 20:04:56.30996 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-31 20:04:56.360915 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-31 20:04:56.414312 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-31 20:04:56.470037 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-31 20:04:56.520299 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-31 20:04:56.571199 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-31 20:04:56.620201 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-31 20:04:56.674204 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-31 20:04:56.742214 INFO::Counting total values for each feature
2026-03-31 20:04:56.754441 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-03-31 20:04:56.804462 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-03-31 20:04:56.865801 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-03-31 20:04:56.930563 INFO::Writing residuals to file output/fits/residuals.rds
2026-03-31 20:04:56.958664 INFO::Writing fitted values to file output/fits/fitted.rds
2026-03-31 20:04:56.973344 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-03-31 20:04:56.976568 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-03-31 20:04:56.97956 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"
2026-03-31 20:04:56.985159 INFO::Writing function arguments to log file
2026-03-31 20:04:56.988991 INFO::Verifying options selected are valid
2026-03-31 20:04:56.989526 INFO::Determining format of input files
2026-03-31 20:04:56.990082 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 20:04:56.992537 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-31 20:04:56.993059 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-03-31 20:04:56.993799 INFO::Filter data based on min abundance and min prevalence
2026-03-31 20:04:56.994246 INFO::Total samples in data: 1595
2026-03-31 20:04:56.994666 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-31 20:04:56.996211 INFO::Total filtered features: 0
2026-03-31 20:04:56.996813 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-31 20:04:56.999529 INFO::Total filtered features with variance filtering: 0
2026-03-31 20:04:57.00005 INFO::Filtered feature names from variance filtering:
2026-03-31 20:04:57.00051 INFO::Running selected normalization method: NONE
2026-03-31 20:04:57.000947 INFO::Bypass z-score application to metadata
2026-03-31 20:04:57.001316 INFO::Running selected transform method: AST
2026-03-31 20:04:57.006896 INFO::Running selected analysis method: LM
2026-03-31 20:04:57.007636 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-31 20:04:57.065135 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-31 20:04:57.118634 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-31 20:04:57.164489 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-31 20:04:57.325839 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-31 20:04:57.376557 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-31 20:04:57.42887 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-31 20:04:57.483326 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-31 20:04:57.538897 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-31 20:04:57.592725 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-31 20:04:57.647794 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-31 20:04:57.69924 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-31 20:04:57.754541 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-31 20:04:57.806945 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-31 20:04:57.857593 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-31 20:04:57.910846 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-31 20:04:57.954419 WARNING::Fitting problem for feature 16 a warning was issued
2026-03-31 20:04:58.013257 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-31 20:04:58.068977 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-31 20:04:58.121085 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-31 20:04:58.171158 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-31 20:04:58.225715 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-31 20:04:58.277402 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-31 20:04:58.330672 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-31 20:04:58.383072 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-31 20:04:58.439917 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-31 20:04:58.490035 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-31 20:04:58.541589 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-31 20:04:58.597471 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-31 20:04:58.654838 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-31 20:04:58.702127 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-31 20:04:58.754205 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-31 20:04:58.808153 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-31 20:04:58.864055 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-31 20:04:58.912649 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-31 20:04:58.963421 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-31 20:04:59.012409 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-31 20:04:59.065176 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-31 20:04:59.117026 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-31 20:04:59.170979 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-31 20:04:59.216393 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-31 20:04:59.268397 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-31 20:04:59.323273 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-31 20:04:59.375957 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-31 20:04:59.427822 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-31 20:04:59.483476 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-31 20:04:59.53371 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-31 20:04:59.587932 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-31 20:04:59.637032 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-31 20:04:59.696058 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-31 20:04:59.750399 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-31 20:04:59.79663 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-31 20:04:59.850066 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-31 20:04:59.896404 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-31 20:04:59.940344 WARNING::Fitting problem for feature 53 a warning was issued
2026-03-31 20:04:59.991126 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-31 20:05:00.038459 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-31 20:05:00.087557 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-31 20:05:00.141359 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-31 20:05:00.191504 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-31 20:05:00.2411 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-31 20:05:00.291042 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-31 20:05:00.340947 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-31 20:05:00.390261 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-31 20:05:00.438078 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-31 20:05:00.488074 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-31 20:05:00.54466 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-31 20:05:00.600832 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-31 20:05:00.653932 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-31 20:05:00.708459 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-31 20:05:00.757529 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-31 20:05:00.811222 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-31 20:05:00.865399 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-31 20:05:00.921973 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-31 20:05:00.93984 WARNING::Fitting problem for feature 72 a warning was issued
2026-03-31 20:05:00.997758 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-31 20:05:01.047626 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-31 20:05:01.110455 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-31 20:05:01.171279 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-31 20:05:01.234704 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-31 20:05:01.304486 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-31 20:05:01.368232 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-31 20:05:01.447999 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-31 20:05:01.514719 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-31 20:05:01.583895 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-31 20:05:01.633464 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-31 20:05:01.686138 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-31 20:05:01.745719 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-31 20:05:01.796472 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-31 20:05:01.851246 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-31 20:05:01.923255 INFO::Counting total values for each feature
2026-03-31 20:05:01.932224 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-03-31 20:05:01.983574 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-03-31 20:05:02.035846 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-03-31 20:05:02.107751 INFO::Writing residuals to file output2/fits/residuals.rds
2026-03-31 20:05:02.158798 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-03-31 20:05:02.205459 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-03-31 20:05:02.209966 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-03-31 20:05:02.213901 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 11.531   0.281  11.928

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	40.986	0.726	42.210