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This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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: 2025-04-21 13:40 -0400 (Mon, 21 Apr 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 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on lconway

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: 2025-04-21 21:36:33 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 21:39:29 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 176.2 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 4.5.0 RC (2025-04-04 r88126)
* 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 94.513  1.785   97.11
* 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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"
2025-04-21 21:38:49.485224 INFO::Writing function arguments to log file
2025-04-21 21:38:49.536091 INFO::Verifying options selected are valid
2025-04-21 21:38:49.57699 INFO::Determining format of input files
2025-04-21 21:38:49.579526 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 21:38:49.5882 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-21 21:38:49.59011 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-21 21:38:49.592506 INFO::Filter data based on min abundance and min prevalence
2025-04-21 21:38:49.593538 INFO::Total samples in data: 1595
2025-04-21 21:38:49.594487 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-21 21:38:49.606933 INFO::Total filtered features: 0
2025-04-21 21:38:49.60897 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 21:38:49.618246 INFO::Total filtered features with variance filtering: 0
2025-04-21 21:38:49.619571 INFO::Filtered feature names from variance filtering:
2025-04-21 21:38:49.621061 INFO::Running selected normalization method: TSS
2025-04-21 21:38:50.786365 INFO::Bypass z-score application to metadata
2025-04-21 21:38:50.787736 INFO::Running selected transform method: AST
2025-04-21 21:38:50.807688 INFO::Running selected analysis method: LM
2025-04-21 21:38:51.453706 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-21 21:38:51.839881 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-21 21:38:52.024479 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-21 21:38:52.205137 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-21 21:38:52.382305 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-21 21:38:52.559905 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-21 21:38:52.714382 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-21 21:38:52.875802 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-21 21:38:53.048305 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-21 21:38:53.215069 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-21 21:38:53.381232 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-21 21:38:53.558544 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-21 21:38:53.722236 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-21 21:38:53.851781 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-21 21:38:54.065546 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-21 21:38:54.219802 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-21 21:38:54.365632 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-21 21:38:54.535844 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-21 21:38:54.703282 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-21 21:38:54.873849 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-21 21:38:55.032193 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-21 21:38:55.217779 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-21 21:38:55.378203 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-21 21:38:55.551519 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-21 21:38:55.726048 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-21 21:38:55.882517 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-21 21:38:56.045819 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-21 21:38:56.207112 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-21 21:38:56.37156 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-21 21:38:56.51962 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-21 21:38:56.700501 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-21 21:38:56.858978 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-21 21:38:57.026418 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-21 21:38:57.189301 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-21 21:38:57.344321 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-21 21:38:57.495567 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-21 21:38:57.905362 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-21 21:38:58.06072 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-21 21:38:58.228614 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-21 21:38:58.415531 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-21 21:38:58.558129 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-21 21:38:58.718602 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-21 21:38:58.870783 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-21 21:38:59.042636 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-21 21:38:59.197007 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-21 21:38:59.363098 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-21 21:38:59.523808 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-21 21:38:59.67873 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-21 21:38:59.836336 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-21 21:38:59.992227 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-21 21:39:00.157785 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-21 21:39:00.318639 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-21 21:39:00.482386 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-21 21:39:00.644122 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-21 21:39:00.802851 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-21 21:39:00.974452 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-21 21:39:01.136537 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-21 21:39:01.296343 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-21 21:39:01.452697 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-21 21:39:01.604311 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-21 21:39:01.763116 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-21 21:39:01.921444 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-21 21:39:02.081148 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-21 21:39:02.260579 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-21 21:39:02.424255 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-21 21:39:02.582336 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-21 21:39:02.75022 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-21 21:39:02.904002 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-21 21:39:03.062 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-21 21:39:03.216326 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-21 21:39:03.373564 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-21 21:39:03.544374 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-21 21:39:03.699724 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-21 21:39:03.868305 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-21 21:39:04.0118 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-21 21:39:04.172532 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-21 21:39:04.321658 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-21 21:39:04.497622 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-21 21:39:04.659281 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-21 21:39:04.836533 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-21 21:39:05.000772 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-21 21:39:05.150452 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-21 21:39:05.310738 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-21 21:39:05.493108 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-21 21:39:05.650702 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-21 21:39:05.807808 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-21 21:39:05.957975 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-21 21:39:06.112567 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-21 21:39:06.32579 INFO::Counting total values for each feature
2025-04-21 21:39:06.382095 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-21 21:39:06.517712 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-21 21:39:06.668865 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-21 21:39:06.828941 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-21 21:39:06.892084 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-21 21:39:06.925571 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-21 21:39:06.932046 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-21 21:39:06.940193 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"
2025-04-21 21:39:06.960403 INFO::Writing function arguments to log file
2025-04-21 21:39:06.971098 INFO::Verifying options selected are valid
2025-04-21 21:39:06.972693 INFO::Determining format of input files
2025-04-21 21:39:06.974339 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 21:39:06.982457 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-21 21:39:06.983902 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-21 21:39:06.986104 INFO::Filter data based on min abundance and min prevalence
2025-04-21 21:39:06.987618 INFO::Total samples in data: 1595
2025-04-21 21:39:06.989038 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-21 21:39:06.996227 INFO::Total filtered features: 0
2025-04-21 21:39:06.99855 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 21:39:07.009201 INFO::Total filtered features with variance filtering: 0
2025-04-21 21:39:07.011278 INFO::Filtered feature names from variance filtering:
2025-04-21 21:39:07.012853 INFO::Running selected normalization method: NONE
2025-04-21 21:39:07.014295 INFO::Bypass z-score application to metadata
2025-04-21 21:39:07.015878 INFO::Running selected transform method: AST
2025-04-21 21:39:07.045819 INFO::Running selected analysis method: LM
2025-04-21 21:39:07.04835 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-21 21:39:07.218378 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-21 21:39:07.385932 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-21 21:39:07.537532 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-21 21:39:07.710958 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-21 21:39:07.879371 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-21 21:39:08.03961 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-21 21:39:08.423205 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-21 21:39:08.567567 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-21 21:39:08.720129 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-21 21:39:08.880539 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-21 21:39:09.042879 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-21 21:39:09.173289 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-21 21:39:09.284185 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-21 21:39:09.456231 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-21 21:39:09.586064 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-21 21:39:09.738777 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-21 21:39:09.887353 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-21 21:39:10.045457 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-21 21:39:10.208502 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-21 21:39:10.356368 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-21 21:39:10.508277 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-21 21:39:10.666594 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-21 21:39:10.808956 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-21 21:39:10.95236 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-21 21:39:11.101896 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-21 21:39:11.235471 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-21 21:39:11.379677 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-21 21:39:11.529017 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-21 21:39:11.66527 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-21 21:39:11.816672 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-21 21:39:11.972272 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-21 21:39:12.111497 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-21 21:39:12.263048 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-21 21:39:12.402765 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-21 21:39:12.550366 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-21 21:39:12.692839 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-21 21:39:12.838187 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-21 21:39:13.001456 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-21 21:39:13.132606 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-21 21:39:13.281499 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-21 21:39:13.422043 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-21 21:39:13.579277 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-21 21:39:13.734645 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-21 21:39:13.879138 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-21 21:39:14.017984 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-21 21:39:14.173759 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-21 21:39:14.322304 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-21 21:39:14.472469 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-21 21:39:14.625797 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-21 21:39:14.764141 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-21 21:39:14.90623 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-21 21:39:15.048224 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-21 21:39:15.185951 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-21 21:39:15.32893 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-21 21:39:15.466364 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-21 21:39:15.622601 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-21 21:39:15.754947 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-21 21:39:15.893919 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-21 21:39:16.054964 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-21 21:39:16.210809 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-21 21:39:16.355481 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-21 21:39:16.515451 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-21 21:39:16.673518 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-21 21:39:16.828891 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-21 21:39:16.992381 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-21 21:39:17.156219 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-21 21:39:17.291963 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-21 21:39:17.420642 WARNING::Fitting problem for feature 67 a warning was issued
2025-04-21 21:39:17.59575 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-21 21:39:17.751094 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-21 21:39:17.908516 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-21 21:39:18.093562 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-21 21:39:18.243363 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-21 21:39:18.291628 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-21 21:39:18.4397 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-21 21:39:18.57648 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-21 21:39:18.719966 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-21 21:39:18.881272 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-21 21:39:19.027079 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-21 21:39:19.166478 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-21 21:39:19.322307 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-21 21:39:19.466408 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-21 21:39:19.619963 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-21 21:39:19.774488 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-21 21:39:19.905511 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-21 21:39:20.051818 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-21 21:39:20.195923 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-21 21:39:20.359304 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-21 21:39:20.516858 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-21 21:39:20.703742 INFO::Counting total values for each feature
2025-04-21 21:39:20.726498 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-21 21:39:20.841046 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-21 21:39:20.965421 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-21 21:39:21.107269 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-21 21:39:21.175549 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-21 21:39:21.253973 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-21 21:39:21.261376 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-21 21:39:21.268823 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 
 32.291   0.687  33.160

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin294.513 1.78597.110