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This page was generated on 2025-03-24 12:08 -0400 (Mon, 24 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4763
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4494
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4521
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4448
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4414
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-20 13:00 -0400 (Thu, 20 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2025-03-21 05:02:39 -0400 (Fri, 21 Mar 2025)
EndedAt: 2025-03-21 05:08:13 -0400 (Fri, 21 Mar 2025)
EllapsedTime: 334.2 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 180.13  2.769  195.76
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.15
Current TMB package version is 1.9.17
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
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"
2025-03-21 05:06:56.391361 INFO::Writing function arguments to log file
2025-03-21 05:06:56.481238 INFO::Verifying options selected are valid
2025-03-21 05:06:56.594874 INFO::Determining format of input files
2025-03-21 05:06:56.598 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 05:06:56.613283 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 05:06:56.616484 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-21 05:06:56.623687 INFO::Filter data based on min abundance and min prevalence
2025-03-21 05:06:56.626493 INFO::Total samples in data: 1595
2025-03-21 05:06:56.628701 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 05:06:56.642323 INFO::Total filtered features: 0
2025-03-21 05:06:56.647164 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 05:06:56.679219 INFO::Total filtered features with variance filtering: 0
2025-03-21 05:06:56.68169 INFO::Filtered feature names from variance filtering:
2025-03-21 05:06:56.683839 INFO::Running selected normalization method: TSS
2025-03-21 05:06:58.993251 INFO::Bypass z-score application to metadata
2025-03-21 05:06:58.995048 INFO::Running selected transform method: AST
2025-03-21 05:06:59.032856 INFO::Running selected analysis method: LM
2025-03-21 05:07:00.163245 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 05:07:00.939285 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 05:07:01.288575 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 05:07:01.607261 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 05:07:01.947862 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 05:07:02.273945 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 05:07:02.595917 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 05:07:02.925366 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 05:07:03.256114 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 05:07:03.582801 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 05:07:03.885973 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 05:07:04.230037 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 05:07:04.533378 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 05:07:04.791975 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-21 05:07:05.148146 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 05:07:05.464703 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 05:07:05.795261 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 05:07:06.10494 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 05:07:06.45871 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 05:07:06.774708 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 05:07:07.078465 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 05:07:07.412434 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 05:07:07.747655 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 05:07:08.103273 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 05:07:08.440975 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 05:07:08.785982 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 05:07:09.109345 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 05:07:09.433542 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 05:07:09.832915 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 05:07:10.168492 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 05:07:10.493951 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 05:07:10.835567 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 05:07:11.170114 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 05:07:11.509997 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 05:07:11.880802 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 05:07:12.185146 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 05:07:12.498348 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 05:07:12.838882 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 05:07:13.172572 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 05:07:13.475302 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 05:07:13.808284 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 05:07:14.129225 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 05:07:14.450758 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 05:07:14.760208 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 05:07:15.058493 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 05:07:15.355898 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 05:07:15.661175 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 05:07:15.993698 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 05:07:16.340876 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 05:07:16.710946 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 05:07:17.093067 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 05:07:17.44948 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 05:07:17.761767 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 05:07:18.067747 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 05:07:18.400057 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 05:07:18.699777 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 05:07:19.016423 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 05:07:19.362039 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 05:07:19.668042 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 05:07:19.996653 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 05:07:20.307153 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 05:07:20.620567 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 05:07:21.223256 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 05:07:21.536375 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 05:07:21.84942 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 05:07:22.15741 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 05:07:22.489371 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 05:07:22.810329 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 05:07:23.11053 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 05:07:23.434943 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 05:07:23.76009 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 05:07:24.078629 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 05:07:24.396225 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 05:07:24.695356 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 05:07:25.013174 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 05:07:25.341077 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 05:07:25.655365 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 05:07:25.981545 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 05:07:26.545412 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 05:07:26.88013 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 05:07:27.213981 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 05:07:27.549668 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 05:07:27.910375 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 05:07:28.259556 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 05:07:28.574572 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 05:07:28.894603 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 05:07:29.250394 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 05:07:29.598155 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 05:07:30.008391 INFO::Counting total values for each feature
2025-03-21 05:07:30.107136 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-21 05:07:30.40553 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-21 05:07:30.79696 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-21 05:07:31.191769 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-21 05:07:31.288618 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-21 05:07:31.34816 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-21 05:07:31.359554 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-21 05:07:31.375992 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"
2025-03-21 05:07:31.408127 INFO::Writing function arguments to log file
2025-03-21 05:07:31.423945 INFO::Verifying options selected are valid
2025-03-21 05:07:31.4264 INFO::Determining format of input files
2025-03-21 05:07:31.429284 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 05:07:31.442797 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 05:07:31.445697 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-21 05:07:31.450533 INFO::Filter data based on min abundance and min prevalence
2025-03-21 05:07:31.452917 INFO::Total samples in data: 1595
2025-03-21 05:07:31.455026 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 05:07:31.47836 INFO::Total filtered features: 0
2025-03-21 05:07:31.481266 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 05:07:31.498099 INFO::Total filtered features with variance filtering: 0
2025-03-21 05:07:31.500811 INFO::Filtered feature names from variance filtering:
2025-03-21 05:07:31.503241 INFO::Running selected normalization method: NONE
2025-03-21 05:07:31.505463 INFO::Bypass z-score application to metadata
2025-03-21 05:07:31.507594 INFO::Running selected transform method: AST
2025-03-21 05:07:31.541964 INFO::Running selected analysis method: LM
2025-03-21 05:07:31.54625 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 05:07:31.843339 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 05:07:32.151605 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 05:07:32.461879 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 05:07:32.766856 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 05:07:33.064872 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 05:07:33.375651 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 05:07:33.700126 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 05:07:33.995323 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 05:07:34.294434 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 05:07:34.60899 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 05:07:34.916023 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 05:07:35.231356 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 05:07:35.492729 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-21 05:07:35.830898 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 05:07:36.135896 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 05:07:36.450466 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 05:07:36.739571 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 05:07:37.04568 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 05:07:37.344169 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 05:07:37.646819 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 05:07:37.938565 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 05:07:38.235207 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 05:07:38.540813 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 05:07:38.839322 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 05:07:39.150682 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 05:07:39.453043 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 05:07:39.751865 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 05:07:40.069763 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 05:07:40.362906 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 05:07:40.650526 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 05:07:40.944089 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 05:07:41.253167 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 05:07:41.565284 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 05:07:41.854899 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 05:07:42.161292 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 05:07:42.448886 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 05:07:42.745041 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 05:07:43.037964 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 05:07:43.353327 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 05:07:43.634167 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 05:07:43.922578 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 05:07:44.229125 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 05:07:44.513776 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 05:07:44.807162 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 05:07:45.131013 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 05:07:45.439174 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 05:07:45.752414 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 05:07:46.056086 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 05:07:46.352467 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 05:07:46.643999 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 05:07:46.936324 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 05:07:47.228344 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 05:07:47.512942 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 05:07:47.818668 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 05:07:48.105006 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 05:07:48.406457 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 05:07:48.71614 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 05:07:49.016554 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 05:07:49.323177 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 05:07:49.61888 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 05:07:49.933293 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 05:07:50.312886 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 05:07:50.615264 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 05:07:50.924962 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 05:07:51.243429 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 05:07:51.562135 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 05:07:51.858014 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 05:07:52.09386 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-21 05:07:52.406613 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 05:07:52.711785 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 05:07:53.00802 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 05:07:53.312075 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 05:07:53.606749 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 05:07:53.712392 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-21 05:07:54.022578 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 05:07:54.322842 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 05:07:54.627107 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 05:07:54.923407 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 05:07:55.234682 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 05:07:55.521022 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 05:07:55.815647 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 05:07:56.127178 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 05:07:56.445231 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 05:07:56.744443 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 05:07:57.04707 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 05:07:57.342383 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 05:07:57.653046 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 05:07:57.946765 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 05:07:58.254336 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 05:07:58.653888 INFO::Counting total values for each feature
2025-03-21 05:07:58.74061 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-21 05:07:59.043817 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-21 05:07:59.348344 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-21 05:07:59.725204 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-21 05:07:59.854238 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-21 05:07:59.976567 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-21 05:07:59.987355 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-21 05:08:00.001874 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 
 61.397   1.121  66.418

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2180.130 2.769195.760