Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-09-11 11:40 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 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

Package 1154/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.22.0  (landing page)
Lauren McIver
Snapshot Date: 2025-09-08 13:40 -0400 (Mon, 08 Sep 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_21
git_last_commit: fcec85e
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on kjohnson1

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: 2025-09-10 01:14:53 -0400 (Wed, 10 Sep 2025)
EndedAt: 2025-09-10 01:17:46 -0400 (Wed, 10 Sep 2025)
EllapsedTime: 172.4 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 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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 91.732  1.787  94.306
* 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-arm64/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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"
2025-09-10 01:17:01.773406 INFO::Writing function arguments to log file
2025-09-10 01:17:01.82148 INFO::Verifying options selected are valid
2025-09-10 01:17:01.861475 INFO::Determining format of input files
2025-09-10 01:17:01.863585 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 01:17:01.870663 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-10 01:17:01.87235 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-10 01:17:01.874819 INFO::Filter data based on min abundance and min prevalence
2025-09-10 01:17:01.875835 INFO::Total samples in data: 1595
2025-09-10 01:17:01.876675 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-10 01:17:01.888321 INFO::Total filtered features: 0
2025-09-10 01:17:01.88987 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 01:17:01.898327 INFO::Total filtered features with variance filtering: 0
2025-09-10 01:17:01.899608 INFO::Filtered feature names from variance filtering:
2025-09-10 01:17:01.900456 INFO::Running selected normalization method: TSS
2025-09-10 01:17:03.083023 INFO::Bypass z-score application to metadata
2025-09-10 01:17:03.08483 INFO::Running selected transform method: AST
2025-09-10 01:17:03.10322 INFO::Running selected analysis method: LM
2025-09-10 01:17:03.808322 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-10 01:17:04.3262 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-10 01:17:04.501191 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-10 01:17:04.702342 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-10 01:17:04.88643 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-10 01:17:05.065893 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-10 01:17:05.242819 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-10 01:17:05.426985 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-10 01:17:05.606138 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-10 01:17:05.748282 WARNING::Fitting problem for feature 9 a warning was issued
2025-09-10 01:17:05.94533 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-10 01:17:06.113073 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-10 01:17:06.286493 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-10 01:17:06.500075 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-10 01:17:06.673415 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-10 01:17:06.844664 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-10 01:17:07.024244 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-10 01:17:07.208829 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-10 01:17:07.393947 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-10 01:17:07.578666 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-10 01:17:07.768684 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-10 01:17:07.943837 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-10 01:17:08.115214 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-10 01:17:08.29596 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-10 01:17:08.459658 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-10 01:17:08.635814 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-10 01:17:08.809686 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-10 01:17:08.990129 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-10 01:17:09.175749 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-10 01:17:09.351626 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-10 01:17:09.542086 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-10 01:17:09.710515 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-10 01:17:09.890599 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-10 01:17:10.081956 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-10 01:17:10.270089 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-10 01:17:10.436474 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-10 01:17:10.629092 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-10 01:17:10.811756 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-10 01:17:11.000769 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-10 01:17:11.174556 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-10 01:17:11.345314 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-10 01:17:11.54055 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-10 01:17:11.721332 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-10 01:17:11.905013 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-10 01:17:12.088898 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-10 01:17:12.261046 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-10 01:17:12.449888 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-10 01:17:12.627662 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-10 01:17:12.814013 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-10 01:17:12.999538 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-10 01:17:13.169316 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-10 01:17:13.339448 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-10 01:17:13.503287 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-10 01:17:13.685088 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-10 01:17:13.865033 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-10 01:17:14.039113 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-10 01:17:14.215066 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-10 01:17:14.407585 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-10 01:17:14.57093 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-10 01:17:14.759385 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-10 01:17:14.930903 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-10 01:17:15.115754 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-10 01:17:15.300833 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-10 01:17:15.485733 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-10 01:17:15.667715 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-10 01:17:15.87485 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-10 01:17:16.039401 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-10 01:17:16.212058 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-10 01:17:16.37932 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-10 01:17:16.845695 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-10 01:17:17.025918 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-10 01:17:17.199786 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-10 01:17:17.376832 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-10 01:17:17.548029 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-10 01:17:17.724859 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-10 01:17:18.184011 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-10 01:17:18.354716 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-10 01:17:18.532038 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-10 01:17:18.717359 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-10 01:17:18.915938 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-10 01:17:19.096074 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-10 01:17:19.263482 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-10 01:17:19.441349 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-10 01:17:19.624411 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-10 01:17:19.785678 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-10 01:17:19.961925 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-10 01:17:20.139025 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-10 01:17:20.315118 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-10 01:17:20.52985 INFO::Counting total values for each feature
2025-09-10 01:17:20.567612 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-10 01:17:20.714585 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-10 01:17:20.887218 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-10 01:17:21.06352 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-10 01:17:21.145227 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-10 01:17:21.189616 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-10 01:17:21.199256 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-10 01:17:21.20826 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"
2025-09-10 01:17:21.224455 INFO::Writing function arguments to log file
2025-09-10 01:17:21.230857 INFO::Verifying options selected are valid
2025-09-10 01:17:21.232012 INFO::Determining format of input files
2025-09-10 01:17:21.233308 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 01:17:21.239654 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-10 01:17:21.240911 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-09-10 01:17:21.242577 INFO::Filter data based on min abundance and min prevalence
2025-09-10 01:17:21.243485 INFO::Total samples in data: 1595
2025-09-10 01:17:21.24429 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-10 01:17:21.248572 INFO::Total filtered features: 0
2025-09-10 01:17:21.249802 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 01:17:21.271171 INFO::Total filtered features with variance filtering: 0
2025-09-10 01:17:21.272876 INFO::Filtered feature names from variance filtering:
2025-09-10 01:17:21.273845 INFO::Running selected normalization method: NONE
2025-09-10 01:17:21.274727 INFO::Bypass z-score application to metadata
2025-09-10 01:17:21.275549 INFO::Running selected transform method: AST
2025-09-10 01:17:21.29172 INFO::Running selected analysis method: LM
2025-09-10 01:17:21.293775 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-10 01:17:21.457914 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-10 01:17:21.623478 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-10 01:17:21.787745 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-10 01:17:21.968809 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-10 01:17:22.133279 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-10 01:17:22.312952 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-10 01:17:22.485315 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-10 01:17:22.665221 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-10 01:17:22.833926 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-10 01:17:22.999441 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-10 01:17:23.138076 WARNING::Fitting problem for feature 11 a warning was issued
2025-09-10 01:17:23.328467 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-10 01:17:23.485753 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-10 01:17:23.621217 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-10 01:17:23.792164 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-10 01:17:23.963306 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-10 01:17:24.127773 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-10 01:17:24.285661 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-10 01:17:24.45297 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-10 01:17:24.623658 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-10 01:17:24.77672 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-10 01:17:24.947752 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-10 01:17:25.127634 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-10 01:17:25.296915 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-10 01:17:25.457248 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-10 01:17:25.62974 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-10 01:17:26.107639 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-10 01:17:26.272071 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-10 01:17:26.438282 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-10 01:17:26.594667 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-10 01:17:26.767148 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-10 01:17:26.928481 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-10 01:17:27.091529 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-10 01:17:27.259188 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-10 01:17:27.451372 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-10 01:17:27.612054 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-10 01:17:27.780978 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-10 01:17:27.954753 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-10 01:17:28.138637 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-10 01:17:28.300774 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-10 01:17:28.461625 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-10 01:17:28.616952 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-10 01:17:28.790817 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-10 01:17:28.947935 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-10 01:17:29.113351 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-10 01:17:29.278696 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-10 01:17:29.45371 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-10 01:17:29.619702 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-10 01:17:29.774543 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-10 01:17:29.939358 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-10 01:17:30.099644 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-10 01:17:30.260371 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-10 01:17:30.425274 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-10 01:17:30.576932 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-10 01:17:30.729022 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-10 01:17:30.901429 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-10 01:17:31.064784 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-10 01:17:31.230109 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-10 01:17:31.389243 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-10 01:17:31.559877 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-10 01:17:31.722696 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-10 01:17:31.876275 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-10 01:17:32.034118 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-10 01:17:32.204191 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-10 01:17:32.360697 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-10 01:17:32.517722 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-10 01:17:32.678037 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-10 01:17:32.84732 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-10 01:17:33.009143 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-10 01:17:33.165588 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-10 01:17:33.336702 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-10 01:17:33.534688 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-10 01:17:33.698552 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-10 01:17:33.758207 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-10 01:17:33.929031 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-10 01:17:34.091905 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-10 01:17:34.270065 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-10 01:17:34.4314 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-10 01:17:34.606826 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-10 01:17:34.769987 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-10 01:17:34.94939 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-10 01:17:35.121232 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-10 01:17:35.292219 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-10 01:17:35.477175 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-10 01:17:35.656373 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-10 01:17:35.807311 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-10 01:17:35.96449 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-10 01:17:36.123506 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-10 01:17:36.304853 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-10 01:17:36.491089 INFO::Counting total values for each feature
2025-09-10 01:17:36.518547 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-10 01:17:36.663373 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-10 01:17:36.808865 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-10 01:17:36.992249 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-10 01:17:37.104273 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-10 01:17:37.21017 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-10 01:17:37.219568 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-10 01:17:37.226676 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 
 35.956   0.801  36.802

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin291.732 1.78794.306