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This page was generated on 2025-08-11 11:46 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-07 13:40 -0400 (Thu, 07 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 2025-08-09 00:44:40 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 00:47:33 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 173.6 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 94.39  1.785  96.487
* 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"
2025-08-09 00:46:49.495818 INFO::Writing function arguments to log file
2025-08-09 00:46:49.544527 INFO::Verifying options selected are valid
2025-08-09 00:46:49.588199 INFO::Determining format of input files
2025-08-09 00:46:49.590532 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-09 00:46:49.59794 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-09 00:46:49.599727 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-09 00:46:49.602354 INFO::Filter data based on min abundance and min prevalence
2025-08-09 00:46:49.603502 INFO::Total samples in data: 1595
2025-08-09 00:46:49.604404 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-09 00:46:49.617645 INFO::Total filtered features: 0
2025-08-09 00:46:49.61941 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-09 00:46:49.628917 INFO::Total filtered features with variance filtering: 0
2025-08-09 00:46:49.630397 INFO::Filtered feature names from variance filtering:
2025-08-09 00:46:49.631293 INFO::Running selected normalization method: TSS
2025-08-09 00:46:50.85048 INFO::Bypass z-score application to metadata
2025-08-09 00:46:50.852265 INFO::Running selected transform method: AST
2025-08-09 00:46:50.869876 INFO::Running selected analysis method: LM
2025-08-09 00:46:51.580009 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-09 00:46:52.110567 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-09 00:46:52.286693 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-09 00:46:52.491149 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-09 00:46:52.675328 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-09 00:46:52.847609 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-09 00:46:53.019514 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-09 00:46:53.19846 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-09 00:46:53.332764 WARNING::Fitting problem for feature 8 a warning was issued
2025-08-09 00:46:53.509791 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-09 00:46:53.663454 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-09 00:46:53.852952 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-09 00:46:54.025987 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-09 00:46:54.256767 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-09 00:46:54.428443 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-09 00:46:54.605891 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-09 00:46:54.779229 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-09 00:46:54.969026 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-09 00:46:55.140361 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-09 00:46:55.316915 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-09 00:46:55.507168 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-09 00:46:55.676153 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-09 00:46:55.844972 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-09 00:46:56.309193 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-09 00:46:56.479454 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-09 00:46:56.659686 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-09 00:46:56.845375 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-09 00:46:57.030082 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-09 00:46:57.192935 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-09 00:46:57.37015 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-09 00:46:57.557709 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-09 00:46:57.72833 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-09 00:46:57.891138 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-09 00:46:58.079201 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-09 00:46:58.253548 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-09 00:46:58.429585 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-09 00:46:58.608695 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-09 00:46:58.773836 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-09 00:46:58.943568 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-09 00:46:59.130766 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-09 00:46:59.287064 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-09 00:46:59.451878 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-09 00:46:59.636312 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-09 00:46:59.811361 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-09 00:46:59.985185 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-09 00:47:00.161513 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-09 00:47:00.327113 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-09 00:47:00.515488 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-09 00:47:00.693962 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-09 00:47:00.865765 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-09 00:47:01.027324 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-09 00:47:01.208827 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-09 00:47:01.376351 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-09 00:47:01.552752 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-09 00:47:01.719195 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-09 00:47:01.893983 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-09 00:47:02.061119 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-09 00:47:02.231581 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-09 00:47:02.416954 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-09 00:47:02.574971 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-09 00:47:02.755 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-09 00:47:02.922881 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-09 00:47:03.103794 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-09 00:47:03.268496 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-09 00:47:03.451645 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-09 00:47:03.63352 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-09 00:47:03.808605 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-09 00:47:03.973976 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-09 00:47:04.151292 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-09 00:47:04.317674 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-09 00:47:04.484709 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-09 00:47:04.686165 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-09 00:47:04.860428 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-09 00:47:05.023901 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-09 00:47:05.206932 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-09 00:47:05.374365 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-09 00:47:05.544156 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-09 00:47:05.733144 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-09 00:47:05.914329 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-09 00:47:06.08974 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-09 00:47:06.290892 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-09 00:47:06.468386 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-09 00:47:06.636561 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-09 00:47:06.839458 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-09 00:47:07.01535 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-09 00:47:07.182036 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-09 00:47:07.364975 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-09 00:47:07.522095 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-09 00:47:07.686681 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-09 00:47:07.913091 INFO::Counting total values for each feature
2025-08-09 00:47:07.953056 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-09 00:47:08.100572 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-09 00:47:08.272682 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-09 00:47:08.455452 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-09 00:47:08.537727 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-09 00:47:08.583079 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-09 00:47:08.593082 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-09 00:47:08.603026 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"
2025-08-09 00:47:08.621624 INFO::Writing function arguments to log file
2025-08-09 00:47:08.628726 INFO::Verifying options selected are valid
2025-08-09 00:47:08.629919 INFO::Determining format of input files
2025-08-09 00:47:08.631302 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-09 00:47:08.638035 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-09 00:47:08.639492 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-09 00:47:08.641213 INFO::Filter data based on min abundance and min prevalence
2025-08-09 00:47:08.642261 INFO::Total samples in data: 1595
2025-08-09 00:47:08.643147 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-09 00:47:08.647928 INFO::Total filtered features: 0
2025-08-09 00:47:08.649309 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-09 00:47:08.6583 INFO::Total filtered features with variance filtering: 0
2025-08-09 00:47:08.659884 INFO::Filtered feature names from variance filtering:
2025-08-09 00:47:08.660799 INFO::Running selected normalization method: NONE
2025-08-09 00:47:08.661606 INFO::Bypass z-score application to metadata
2025-08-09 00:47:08.662399 INFO::Running selected transform method: AST
2025-08-09 00:47:08.686988 INFO::Running selected analysis method: LM
2025-08-09 00:47:08.690039 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-09 00:47:08.863338 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-09 00:47:09.0485 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-09 00:47:09.202175 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-09 00:47:09.658636 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-09 00:47:09.818832 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-09 00:47:09.992581 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-09 00:47:10.165748 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-09 00:47:10.336137 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-09 00:47:10.470561 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-09 00:47:10.642681 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-09 00:47:10.822444 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-09 00:47:10.987998 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-09 00:47:11.148066 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-09 00:47:11.28276 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-09 00:47:11.466228 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-09 00:47:11.632131 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-09 00:47:11.796575 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-09 00:47:11.924285 WARNING::Fitting problem for feature 16 a warning was issued
2025-08-09 00:47:12.096784 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-09 00:47:12.260537 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-09 00:47:12.42165 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-09 00:47:12.58688 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-09 00:47:12.747134 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-09 00:47:12.909041 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-09 00:47:13.079062 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-09 00:47:13.24152 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-09 00:47:13.40556 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-09 00:47:13.570628 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-09 00:47:13.741915 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-09 00:47:13.906853 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-09 00:47:14.065227 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-09 00:47:14.234795 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-09 00:47:14.395343 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-09 00:47:14.561229 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-09 00:47:14.751869 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-09 00:47:14.911285 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-09 00:47:15.076406 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-09 00:47:15.247599 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-09 00:47:15.413917 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-09 00:47:15.577995 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-09 00:47:15.752934 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-09 00:47:15.905631 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-09 00:47:16.061638 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-09 00:47:16.236345 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-09 00:47:16.391571 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-09 00:47:16.55916 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-09 00:47:16.740247 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-09 00:47:16.9032 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-09 00:47:17.073222 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-09 00:47:17.236719 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-09 00:47:17.420208 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-09 00:47:17.581104 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-09 00:47:17.734285 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-09 00:47:17.91287 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-09 00:47:18.060398 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-09 00:47:18.21098 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-09 00:47:18.36765 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-09 00:47:18.535002 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-09 00:47:18.692374 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-09 00:47:18.851371 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-09 00:47:19.0186 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-09 00:47:19.180128 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-09 00:47:19.335187 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-09 00:47:19.504469 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-09 00:47:19.660272 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-09 00:47:19.821545 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-09 00:47:19.995165 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-09 00:47:20.156276 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-09 00:47:20.317071 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-09 00:47:20.50069 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-09 00:47:20.66196 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-09 00:47:20.831165 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-09 00:47:21.020107 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-09 00:47:21.189285 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-09 00:47:21.246807 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-09 00:47:21.422397 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-09 00:47:21.584897 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-09 00:47:21.745855 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-09 00:47:21.915094 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-09 00:47:22.076082 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-09 00:47:22.244973 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-09 00:47:22.406897 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-09 00:47:22.582782 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-09 00:47:22.738734 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-09 00:47:22.909666 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-09 00:47:23.080618 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-09 00:47:23.237241 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-09 00:47:23.405531 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-09 00:47:23.567658 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-09 00:47:23.740894 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-09 00:47:23.937655 INFO::Counting total values for each feature
2025-08-09 00:47:23.964136 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-09 00:47:24.109181 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-09 00:47:24.254887 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-09 00:47:24.425084 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-09 00:47:24.535775 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-09 00:47:24.657722 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-09 00:47:24.667499 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-09 00:47:24.674914 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 35.790   0.733  36.564

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin294.390 1.78596.487