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This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4493
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 1142/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 43d70cc
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 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
kjohnson3macOS 13.7.1 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 nebbiolo2

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: 1.23.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz
StartedAt: 2025-06-19 00:30:35 -0400 (Thu, 19 Jun 2025)
EndedAt: 2025-06-19 00:34:47 -0400 (Thu, 19 Jun 2025)
EllapsedTime: 252.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.23.0’
* 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 loading without being on the library search path ... 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 87.302  0.865  88.157
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.23.0’
** 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 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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"
2025-06-19 00:32:32.740386 INFO::Writing function arguments to log file
2025-06-19 00:32:32.780798 INFO::Verifying options selected are valid
2025-06-19 00:32:32.814658 INFO::Determining format of input files
2025-06-19 00:32:32.816203 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-19 00:32:32.821143 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-06-19 00:32:32.82241 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-06-19 00:32:32.824768 INFO::Filter data based on min abundance and min prevalence
2025-06-19 00:32:32.825635 INFO::Total samples in data: 1595
2025-06-19 00:32:32.826466 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-06-19 00:32:32.836813 INFO::Total filtered features: 0
2025-06-19 00:32:32.838073 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-19 00:32:32.844425 INFO::Total filtered features with variance filtering: 0
2025-06-19 00:32:32.845455 INFO::Filtered feature names from variance filtering:
2025-06-19 00:32:32.846289 INFO::Running selected normalization method: TSS
2025-06-19 00:32:33.886251 INFO::Bypass z-score application to metadata
2025-06-19 00:32:33.887825 INFO::Running selected transform method: AST
2025-06-19 00:32:33.905276 INFO::Running selected analysis method: LM
2025-06-19 00:32:34.513417 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-06-19 00:32:34.973032 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-06-19 00:32:35.122972 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-06-19 00:32:35.285806 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-06-19 00:32:35.432249 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-06-19 00:32:35.578092 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-06-19 00:32:35.72524 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-06-19 00:32:35.87843 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-06-19 00:32:35.99324 WARNING::Fitting problem for feature 8 a warning was issued
2025-06-19 00:32:36.145183 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-06-19 00:32:36.266157 WARNING::Fitting problem for feature 9 a warning was issued
2025-06-19 00:32:36.430733 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-06-19 00:32:36.57146 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-06-19 00:32:36.749542 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-06-19 00:32:36.890678 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-06-19 00:32:37.01137 WARNING::Fitting problem for feature 13 a warning was issued
2025-06-19 00:32:37.167514 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-06-19 00:32:37.326506 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-06-19 00:32:37.505302 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-06-19 00:32:37.656023 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-06-19 00:32:37.825997 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-06-19 00:32:37.982577 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-06-19 00:32:38.121825 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-06-19 00:32:38.272841 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-06-19 00:32:38.420017 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-06-19 00:32:38.567243 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-06-19 00:32:38.706496 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-06-19 00:32:38.858067 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-06-19 00:32:39.008086 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-06-19 00:32:39.1562 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-06-19 00:32:39.317176 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-06-19 00:32:39.462314 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-06-19 00:32:39.60907 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-06-19 00:32:39.758855 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-06-19 00:32:39.906043 INFO::Fitting model to feature number 32, Prevotella.copri
2025-06-19 00:32:40.047063 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-06-19 00:32:40.199689 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-06-19 00:32:40.335417 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-06-19 00:32:40.481892 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-06-19 00:32:40.624246 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-06-19 00:32:40.787552 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-06-19 00:32:40.95394 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-06-19 00:32:41.104443 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-06-19 00:32:41.255573 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-06-19 00:32:41.409329 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-06-19 00:32:41.562578 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-06-19 00:32:41.715464 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-06-19 00:32:41.854812 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-06-19 00:32:41.996726 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-06-19 00:32:42.153099 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-06-19 00:32:42.302383 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-06-19 00:32:42.449522 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-06-19 00:32:42.591845 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-06-19 00:32:42.748198 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-06-19 00:32:42.892997 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-06-19 00:32:43.052311 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-06-19 00:32:43.207094 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-06-19 00:32:43.355478 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-06-19 00:32:43.507221 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-06-19 00:32:43.674561 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-06-19 00:32:43.81522 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-06-19 00:32:43.966702 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-06-19 00:32:44.107363 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-06-19 00:32:44.254733 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-06-19 00:32:44.403514 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-06-19 00:32:44.565916 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-06-19 00:32:44.7447 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-06-19 00:32:44.885941 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-06-19 00:32:45.027724 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-06-19 00:32:45.191118 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-06-19 00:32:45.331377 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-06-19 00:32:45.480117 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-06-19 00:32:45.639262 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-06-19 00:32:45.806087 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-06-19 00:32:45.956706 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-06-19 00:32:46.118564 INFO::Fitting model to feature number 73, Dialister.invisus
2025-06-19 00:32:46.299001 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-06-19 00:32:46.456585 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-06-19 00:32:46.603114 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-06-19 00:32:46.758459 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-06-19 00:32:46.907751 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-06-19 00:32:47.065001 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-06-19 00:32:47.228539 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-06-19 00:32:47.372434 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-06-19 00:32:47.533422 INFO::Fitting model to feature number 82, Escherichia.coli
2025-06-19 00:32:47.682371 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-06-19 00:32:47.829688 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-06-19 00:32:47.989908 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-06-19 00:32:48.142294 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-06-19 00:32:48.286643 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-06-19 00:32:48.492468 INFO::Counting total values for each feature
2025-06-19 00:32:48.526275 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-06-19 00:32:48.61997 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-06-19 00:32:48.715032 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-06-19 00:32:48.813209 INFO::Writing residuals to file output/fits/residuals.rds
2025-06-19 00:32:48.861571 INFO::Writing fitted values to file output/fits/fitted.rds
2025-06-19 00:32:49.165744 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-06-19 00:32:49.172427 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-06-19 00:32:49.177496 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"
2025-06-19 00:32:49.190487 INFO::Writing function arguments to log file
2025-06-19 00:32:49.196474 INFO::Verifying options selected are valid
2025-06-19 00:32:49.197489 INFO::Determining format of input files
2025-06-19 00:32:49.198757 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-19 00:32:49.204296 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-06-19 00:32:49.20541 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-06-19 00:32:49.207052 INFO::Filter data based on min abundance and min prevalence
2025-06-19 00:32:49.207919 INFO::Total samples in data: 1595
2025-06-19 00:32:49.208772 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-06-19 00:32:49.21289 INFO::Total filtered features: 0
2025-06-19 00:32:49.213847 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-19 00:32:49.220333 INFO::Total filtered features with variance filtering: 0
2025-06-19 00:32:49.221352 INFO::Filtered feature names from variance filtering:
2025-06-19 00:32:49.222194 INFO::Running selected normalization method: NONE
2025-06-19 00:32:49.222985 INFO::Bypass z-score application to metadata
2025-06-19 00:32:49.223804 INFO::Running selected transform method: AST
2025-06-19 00:32:49.238227 INFO::Running selected analysis method: LM
2025-06-19 00:32:49.2398 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-06-19 00:32:49.380282 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-06-19 00:32:49.526875 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-06-19 00:32:49.663616 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-06-19 00:32:49.802578 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-06-19 00:32:49.938723 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-06-19 00:32:50.087808 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-06-19 00:32:50.225528 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-06-19 00:32:50.361514 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-06-19 00:32:50.506863 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-06-19 00:32:50.645688 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-06-19 00:32:50.761047 WARNING::Fitting problem for feature 11 a warning was issued
2025-06-19 00:32:50.906 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-06-19 00:32:51.050988 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-06-19 00:32:51.191339 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-06-19 00:32:51.329443 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-06-19 00:32:51.47893 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-06-19 00:32:51.590266 WARNING::Fitting problem for feature 16 a warning was issued
2025-06-19 00:32:51.735992 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-06-19 00:32:51.887751 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-06-19 00:32:52.034527 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-06-19 00:32:52.174804 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-06-19 00:32:52.319413 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-06-19 00:32:52.457141 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-06-19 00:32:52.59389 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-06-19 00:32:52.731878 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-06-19 00:32:52.871931 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-06-19 00:32:53.009131 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-06-19 00:32:53.156452 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-06-19 00:32:53.302117 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-06-19 00:32:53.439455 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-06-19 00:32:53.571065 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-06-19 00:32:53.713984 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-06-19 00:32:54.116737 INFO::Fitting model to feature number 32, Prevotella.copri
2025-06-19 00:32:54.267778 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-06-19 00:32:54.412914 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-06-19 00:32:54.559966 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-06-19 00:32:54.705157 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-06-19 00:32:54.842019 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-06-19 00:32:54.98058 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-06-19 00:32:55.119828 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-06-19 00:32:55.262339 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-06-19 00:32:55.39426 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-06-19 00:32:55.52873 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-06-19 00:32:55.670195 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-06-19 00:32:55.805528 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-06-19 00:32:55.943944 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-06-19 00:32:56.078028 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-06-19 00:32:56.223987 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-06-19 00:32:56.353481 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-06-19 00:32:56.494058 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-06-19 00:32:56.628524 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-06-19 00:32:56.761799 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-06-19 00:32:56.89993 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-06-19 00:32:57.030894 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-06-19 00:32:57.165376 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-06-19 00:32:57.296611 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-06-19 00:32:57.426486 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-06-19 00:32:57.560819 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-06-19 00:32:57.70012 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-06-19 00:32:57.83083 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-06-19 00:32:57.968176 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-06-19 00:32:58.103378 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-06-19 00:32:58.236553 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-06-19 00:32:58.371537 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-06-19 00:32:58.516092 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-06-19 00:32:58.649368 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-06-19 00:32:58.785031 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-06-19 00:32:58.925203 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-06-19 00:32:59.03795 WARNING::Fitting problem for feature 67 a warning was issued
2025-06-19 00:32:59.185808 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-06-19 00:32:59.324458 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-06-19 00:32:59.485796 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-06-19 00:32:59.650038 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-06-19 00:32:59.807721 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-06-19 00:32:59.856803 WARNING::Fitting problem for feature 72 a warning was issued
2025-06-19 00:32:59.995156 INFO::Fitting model to feature number 73, Dialister.invisus
2025-06-19 00:33:00.13698 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-06-19 00:33:00.273503 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-06-19 00:33:00.411393 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-06-19 00:33:00.557117 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-06-19 00:33:00.694893 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-06-19 00:33:00.83728 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-06-19 00:33:00.977459 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-06-19 00:33:01.110918 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-06-19 00:33:01.257035 INFO::Fitting model to feature number 82, Escherichia.coli
2025-06-19 00:33:01.389992 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-06-19 00:33:01.534346 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-06-19 00:33:01.670171 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-06-19 00:33:01.813205 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-06-19 00:33:01.950243 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-06-19 00:33:02.114113 INFO::Counting total values for each feature
2025-06-19 00:33:02.135738 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-06-19 00:33:02.228 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-06-19 00:33:02.320326 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-06-19 00:33:02.416424 INFO::Writing residuals to file output2/fits/residuals.rds
2025-06-19 00:33:02.725838 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-06-19 00:33:02.788565 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-06-19 00:33:02.793948 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-06-19 00:33:02.798215 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.690   0.527  31.206

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin287.302 0.86588.157