Multiple platform build/check report for BioC 3.21 - CHECK results for Maaslin2 on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4606
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4547
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 merida1

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: 1.22.0

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_1.22.0.tar.gz

StartedAt: 2025-09-09 05:37:37 -0400 (Tue, 09 Sep 2025)

EndedAt: 2025-09-09 05:43:03 -0400 (Tue, 09 Sep 2025)

EllapsedTime: 325.9 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* 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 181.904  2.588 189.906
* 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.22.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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"
2025-09-09 05:41:46.464606 INFO::Writing function arguments to log file
2025-09-09 05:41:46.552264 INFO::Verifying options selected are valid
2025-09-09 05:41:46.623826 INFO::Determining format of input files
2025-09-09 05:41:46.62747 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 05:41:46.641417 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-09 05:41:46.644783 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-09 05:41:46.651128 INFO::Filter data based on min abundance and min prevalence
2025-09-09 05:41:46.653755 INFO::Total samples in data: 1595
2025-09-09 05:41:46.656414 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-09 05:41:46.676952 INFO::Total filtered features: 0
2025-09-09 05:41:46.679671 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-09 05:41:46.698633 INFO::Total filtered features with variance filtering: 0
2025-09-09 05:41:46.701379 INFO::Filtered feature names from variance filtering:
2025-09-09 05:41:46.703623 INFO::Running selected normalization method: TSS
2025-09-09 05:41:48.835857 INFO::Bypass z-score application to metadata
2025-09-09 05:41:48.838596 INFO::Running selected transform method: AST
2025-09-09 05:41:48.870323 INFO::Running selected analysis method: LM
2025-09-09 05:41:50.045757 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-09 05:41:51.172255 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-09 05:41:51.482925 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-09 05:41:51.827153 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-09 05:41:52.157089 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-09 05:41:52.463937 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-09 05:41:52.763903 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-09 05:41:53.079592 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-09 05:41:53.386058 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-09 05:41:53.684283 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-09 05:41:53.99261 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-09 05:41:54.294713 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-09 05:41:54.596767 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-09 05:41:54.89064 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-09 05:41:55.222437 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-09 05:41:55.533553 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-09 05:41:55.848981 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-09 05:41:56.151716 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-09 05:41:56.469932 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-09 05:41:56.770477 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-09 05:41:57.070318 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-09 05:41:57.382704 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-09 05:41:57.684546 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-09 05:41:57.993209 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-09 05:41:58.281977 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-09 05:41:58.587708 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-09 05:41:58.905423 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-09 05:41:59.200869 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-09 05:41:59.513576 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-09 05:41:59.836345 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-09 05:42:00.141037 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-09 05:42:00.432503 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-09 05:42:00.758397 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-09 05:42:01.058469 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-09 05:42:01.367857 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-09 05:42:01.674271 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-09 05:42:01.983065 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-09 05:42:02.294116 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-09 05:42:02.595069 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-09 05:42:02.876597 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-09 05:42:03.182511 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-09 05:42:03.485063 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-09 05:42:03.791534 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-09 05:42:04.093425 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-09 05:42:04.396195 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-09 05:42:04.692732 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-09 05:42:04.997012 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-09 05:42:05.303032 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-09 05:42:05.612863 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-09 05:42:05.913033 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-09 05:42:06.203084 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-09 05:42:06.502631 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-09 05:42:06.796638 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-09 05:42:07.103624 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-09 05:42:07.42859 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-09 05:42:07.719111 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-09 05:42:08.046286 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-09 05:42:08.349469 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-09 05:42:08.639356 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-09 05:42:08.947638 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-09 05:42:09.239577 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-09 05:42:09.536286 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-09 05:42:10.112237 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-09 05:42:10.423814 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-09 05:42:10.836722 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-09 05:42:11.177076 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-09 05:42:11.476121 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-09 05:42:11.790874 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-09 05:42:12.120907 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-09 05:42:12.431382 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-09 05:42:12.792414 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-09 05:42:13.235459 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-09 05:42:13.661711 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-09 05:42:14.188529 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-09 05:42:14.485122 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-09 05:42:14.801764 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-09 05:42:15.140189 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-09 05:42:15.477066 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-09 05:42:15.801889 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-09 05:42:16.178164 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-09 05:42:16.543565 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-09 05:42:16.876962 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-09 05:42:17.217481 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-09 05:42:17.59362 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-09 05:42:17.964039 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-09 05:42:18.298159 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-09 05:42:18.646567 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-09 05:42:18.9893 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-09 05:42:19.471854 INFO::Counting total values for each feature
2025-09-09 05:42:19.611401 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-09 05:42:20.070327 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-09 05:42:20.865411 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-09 05:42:21.472896 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-09 05:42:21.601399 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-09 05:42:21.658865 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-09 05:42:21.700718 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-09 05:42:21.722149 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"
2025-09-09 05:42:21.760225 INFO::Writing function arguments to log file
2025-09-09 05:42:21.826786 INFO::Verifying options selected are valid
2025-09-09 05:42:21.829512 INFO::Determining format of input files
2025-09-09 05:42:21.874458 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 05:42:21.888439 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-09 05:42:21.924587 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-09-09 05:42:21.93303 INFO::Filter data based on min abundance and min prevalence
2025-09-09 05:42:21.935834 INFO::Total samples in data: 1595
2025-09-09 05:42:21.941135 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-09 05:42:21.951757 INFO::Total filtered features: 0
2025-09-09 05:42:21.955214 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-09 05:42:21.973662 INFO::Total filtered features with variance filtering: 0
2025-09-09 05:42:21.989146 INFO::Filtered feature names from variance filtering:
2025-09-09 05:42:21.991496 INFO::Running selected normalization method: NONE
2025-09-09 05:42:22.035897 INFO::Bypass z-score application to metadata
2025-09-09 05:42:22.077104 INFO::Running selected transform method: AST
2025-09-09 05:42:22.108435 INFO::Running selected analysis method: LM
2025-09-09 05:42:22.149613 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-09 05:42:22.456732 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-09 05:42:22.80328 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-09 05:42:23.087771 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-09 05:42:23.393589 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-09 05:42:23.719128 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-09 05:42:24.046928 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-09 05:42:24.373228 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-09 05:42:24.706539 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-09 05:42:25.026554 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-09 05:42:25.355643 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-09 05:42:25.670354 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-09 05:42:25.991916 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-09 05:42:26.523743 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-09 05:42:26.880004 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-09 05:42:27.166616 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-09 05:42:27.483097 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-09 05:42:27.802628 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-09 05:42:28.115893 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-09 05:42:28.422019 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-09 05:42:28.708041 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-09 05:42:29.026355 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-09 05:42:29.31359 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-09 05:42:29.604457 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-09 05:42:29.888546 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-09 05:42:30.170039 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-09 05:42:30.457818 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-09 05:42:30.743159 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-09 05:42:31.035017 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-09 05:42:31.314821 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-09 05:42:31.584169 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-09 05:42:31.872375 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-09 05:42:32.156631 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-09 05:42:32.434763 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-09 05:42:32.968296 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-09 05:42:33.254468 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-09 05:42:33.526682 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-09 05:42:33.805151 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-09 05:42:34.109279 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-09 05:42:34.39437 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-09 05:42:34.665851 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-09 05:42:34.936171 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-09 05:42:35.226018 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-09 05:42:35.492277 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-09 05:42:35.781118 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-09 05:42:36.084839 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-09 05:42:36.36402 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-09 05:42:36.660195 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-09 05:42:37.225951 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-09 05:42:37.500729 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-09 05:42:37.767545 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-09 05:42:38.039301 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-09 05:42:38.341227 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-09 05:42:38.621915 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-09 05:42:38.88741 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-09 05:42:39.157878 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-09 05:42:39.459073 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-09 05:42:39.742693 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-09 05:42:40.008945 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-09 05:42:40.286289 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-09 05:42:40.567998 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-09 05:42:40.85264 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-09 05:42:41.126263 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-09 05:42:41.390044 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-09 05:42:41.673736 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-09 05:42:41.987635 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-09 05:42:42.274114 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-09 05:42:42.549779 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-09 05:42:42.788608 WARNING::Fitting problem for feature 67 a warning was issued
2025-09-09 05:42:43.165286 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-09 05:42:43.431604 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-09 05:42:43.718559 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-09 05:42:44.018754 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-09 05:42:44.317864 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-09 05:42:44.432072 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-09 05:42:44.726863 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-09 05:42:45.017202 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-09 05:42:45.308342 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-09 05:42:45.599618 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-09 05:42:45.882764 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-09 05:42:46.16088 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-09 05:42:46.441744 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-09 05:42:46.741246 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-09 05:42:47.006267 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-09 05:42:47.290854 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-09 05:42:47.554773 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-09 05:42:47.837503 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-09 05:42:48.133554 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-09 05:42:48.466318 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-09 05:42:48.872194 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-09 05:42:49.323942 INFO::Counting total values for each feature
2025-09-09 05:42:49.38649 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-09 05:42:49.65672 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-09 05:42:49.923672 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-09 05:42:50.256974 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-09 05:42:50.386875 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-09 05:42:50.503087 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-09 05:42:50.514069 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-09 05:42:50.528287 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 
 61.159   1.282  66.580

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	181.904	2.588	189.906