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This page was generated on 2026-03-31 11:57 -0400 (Tue, 31 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4893
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 1169/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.24.1  (landing page)
Sagun Maharjan
Snapshot Date: 2026-03-30 13:45 -0400 (Mon, 30 Mar 2026)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_22
git_last_commit: b4535fa
git_last_commit_date: 2026-03-16 11:24:01 -0400 (Mon, 16 Mar 2026)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for Maaslin2 in R Universe.

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: 1.24.1
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_1.24.1.tar.gz
StartedAt: 2026-03-31 00:49:00 -0400 (Tue, 31 Mar 2026)
EndedAt: 2026-03-31 00:54:27 -0400 (Tue, 31 Mar 2026)
EllapsedTime: 326.4 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_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.24.1’
* 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: no visible binding for global variable ‘var’
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  var xnames
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
* 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 123.254  1.009 125.826
* 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 ‘1.24.1’
** 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 1.9.19
Current TMB package version is 1.9.21
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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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"
2026-03-31 00:51:36.622889 INFO::Writing function arguments to log file
2026-03-31 00:51:36.661624 INFO::Verifying options selected are valid
2026-03-31 00:51:36.694813 INFO::Determining format of input files
2026-03-31 00:51:36.696328 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 00:51:36.701262 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-31 00:51:36.70255 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-03-31 00:51:36.704854 INFO::Filter data based on min abundance and min prevalence
2026-03-31 00:51:36.70574 INFO::Total samples in data: 1595
2026-03-31 00:51:36.706614 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-31 00:51:36.710246 INFO::Total filtered features: 0
2026-03-31 00:51:36.71128 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-31 00:51:36.724676 INFO::Total filtered features with variance filtering: 0
2026-03-31 00:51:36.725851 INFO::Filtered feature names from variance filtering:
2026-03-31 00:51:36.726756 INFO::Running selected normalization method: TSS
2026-03-31 00:51:37.728166 INFO::Bypass z-score application to metadata
2026-03-31 00:51:37.729464 INFO::Running selected transform method: AST
2026-03-31 00:51:37.747426 INFO::Running selected analysis method: LM
2026-03-31 00:51:38.503759 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-31 00:51:39.154099 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-31 00:51:39.334128 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-31 00:51:39.486096 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-31 00:51:39.64835 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-31 00:51:39.820264 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-31 00:51:39.981382 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-31 00:51:40.136672 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-31 00:51:40.262284 WARNING::Fitting problem for feature 8 a warning was issued
2026-03-31 00:51:40.419217 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-31 00:51:40.539997 WARNING::Fitting problem for feature 9 a warning was issued
2026-03-31 00:51:40.760638 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-31 00:51:40.917408 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-31 00:51:41.070397 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-31 00:51:41.653699 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-31 00:51:41.772376 WARNING::Fitting problem for feature 13 a warning was issued
2026-03-31 00:51:41.922264 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-31 00:51:42.071969 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-31 00:51:42.228145 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-31 00:51:42.367177 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-31 00:51:42.519172 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-31 00:51:42.677473 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-31 00:51:42.812036 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-31 00:51:42.95217 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-31 00:51:43.136443 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-31 00:51:43.326994 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-31 00:51:43.476541 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-31 00:51:43.635935 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-31 00:51:43.784056 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-31 00:51:43.919154 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-31 00:51:44.067235 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-31 00:51:44.213589 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-31 00:51:44.366647 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-31 00:51:44.504419 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-31 00:51:44.653892 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-31 00:51:44.828277 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-31 00:51:44.981049 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-31 00:51:45.130182 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-31 00:51:45.279962 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-31 00:51:45.427269 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-31 00:51:45.568923 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-31 00:51:45.701647 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-31 00:51:45.836725 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-31 00:51:45.982821 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-31 00:51:46.121394 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-31 00:51:46.268458 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-31 00:51:46.414154 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-31 00:51:46.549641 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-31 00:51:46.68724 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-31 00:51:46.841888 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-31 00:51:47.007619 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-31 00:51:47.148051 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-31 00:51:47.29579 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-31 00:51:47.441864 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-31 00:51:47.580991 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-31 00:51:47.720517 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-31 00:51:47.867405 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-31 00:51:48.007897 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-31 00:51:48.153079 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-31 00:51:48.307434 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-31 00:51:48.454705 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-31 00:51:48.598145 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-31 00:51:48.737952 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-31 00:51:48.877121 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-31 00:51:49.027446 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-31 00:51:49.1703 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-31 00:51:49.313649 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-31 00:51:49.459938 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-31 00:51:49.598584 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-31 00:51:49.741721 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-31 00:51:49.881728 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-31 00:51:50.026523 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-31 00:51:50.178004 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-31 00:51:50.361784 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-31 00:51:50.51135 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-31 00:51:50.665783 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-31 00:51:50.811311 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-31 00:51:50.948358 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-31 00:51:51.090659 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-31 00:51:51.237951 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-31 00:51:51.380101 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-31 00:51:51.532005 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-31 00:51:51.687233 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-31 00:51:51.829565 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-31 00:51:51.994826 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-31 00:51:52.137102 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-31 00:51:52.278071 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-31 00:51:52.424805 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-31 00:51:52.571982 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-31 00:51:52.725214 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-31 00:51:52.93869 INFO::Counting total values for each feature
2026-03-31 00:51:52.97101 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-03-31 00:51:53.065831 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-03-31 00:51:53.163563 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-03-31 00:51:53.264419 INFO::Writing residuals to file output/fits/residuals.rds
2026-03-31 00:51:53.312572 INFO::Writing fitted values to file output/fits/fitted.rds
2026-03-31 00:51:53.339216 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-03-31 00:51:53.344517 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-03-31 00:51:53.349524 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"
2026-03-31 00:51:53.362686 INFO::Writing function arguments to log file
2026-03-31 00:51:53.368185 INFO::Verifying options selected are valid
2026-03-31 00:51:53.369167 INFO::Determining format of input files
2026-03-31 00:51:53.37037 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 00:51:53.375669 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-31 00:51:53.37671 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-03-31 00:51:53.37825 INFO::Filter data based on min abundance and min prevalence
2026-03-31 00:51:53.379104 INFO::Total samples in data: 1595
2026-03-31 00:51:53.37994 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-31 00:51:53.383856 INFO::Total filtered features: 0
2026-03-31 00:51:53.384799 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-31 00:51:53.391953 INFO::Total filtered features with variance filtering: 0
2026-03-31 00:51:53.393027 INFO::Filtered feature names from variance filtering:
2026-03-31 00:51:53.393853 INFO::Running selected normalization method: NONE
2026-03-31 00:51:53.39466 INFO::Bypass z-score application to metadata
2026-03-31 00:51:53.395466 INFO::Running selected transform method: AST
2026-03-31 00:51:53.41057 INFO::Running selected analysis method: LM
2026-03-31 00:51:53.412084 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-31 00:51:53.552007 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-31 00:51:53.688191 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-31 00:51:53.81719 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-31 00:51:53.955544 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-31 00:51:54.099295 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-31 00:51:54.234504 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-31 00:51:54.370831 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-31 00:51:54.510986 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-31 00:51:54.645418 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-31 00:51:54.784075 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-31 00:51:54.900872 WARNING::Fitting problem for feature 11 a warning was issued
2026-03-31 00:51:55.054704 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-31 00:51:55.181321 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-31 00:51:55.316554 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-31 00:51:55.448366 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-31 00:51:55.596482 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-31 00:51:55.701772 WARNING::Fitting problem for feature 16 a warning was issued
2026-03-31 00:51:55.838372 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-31 00:51:55.990308 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-31 00:51:56.124868 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-31 00:51:56.252123 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-31 00:51:56.387657 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-31 00:51:56.52865 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-31 00:51:56.667418 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-31 00:51:56.797983 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-31 00:51:56.943056 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-31 00:51:57.075086 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-31 00:51:57.205763 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-31 00:51:57.351951 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-31 00:51:57.479287 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-31 00:51:57.606862 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-31 00:51:57.748824 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-31 00:51:57.881834 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-31 00:51:58.012944 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-31 00:51:58.147584 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-31 00:51:58.278764 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-31 00:51:58.407451 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-31 00:51:58.545299 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-31 00:51:58.678483 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-31 00:51:58.813064 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-31 00:51:58.943666 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-31 00:51:59.06799 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-31 00:51:59.204909 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-31 00:51:59.333674 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-31 00:51:59.47049 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-31 00:51:59.618052 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-31 00:51:59.753239 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-31 00:51:59.897037 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-31 00:52:00.027032 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-31 00:52:00.169472 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-31 00:52:00.300967 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-31 00:52:00.431443 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-31 00:52:00.563162 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-31 00:52:00.944661 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-31 00:52:01.063812 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-31 00:52:01.188494 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-31 00:52:01.324135 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-31 00:52:01.463777 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-31 00:52:01.592954 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-31 00:52:01.720601 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-31 00:52:01.851593 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-31 00:52:01.982223 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-31 00:52:02.112684 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-31 00:52:02.240855 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-31 00:52:02.378986 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-31 00:52:02.513058 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-31 00:52:02.647528 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-31 00:52:02.790319 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-31 00:52:02.909084 WARNING::Fitting problem for feature 67 a warning was issued
2026-03-31 00:52:03.050978 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-31 00:52:03.185434 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-31 00:52:03.32791 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-31 00:52:03.480111 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-31 00:52:03.620403 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-31 00:52:03.680522 WARNING::Fitting problem for feature 72 a warning was issued
2026-03-31 00:52:03.840404 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-31 00:52:03.994392 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-31 00:52:04.135086 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-31 00:52:04.27512 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-31 00:52:04.407923 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-31 00:52:04.544896 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-31 00:52:04.680239 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-31 00:52:04.816354 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-31 00:52:04.957286 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-31 00:52:05.097199 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-31 00:52:05.223245 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-31 00:52:05.351798 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-31 00:52:05.486478 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-31 00:52:05.613564 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-31 00:52:05.747114 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-31 00:52:05.911474 INFO::Counting total values for each feature
2026-03-31 00:52:05.933045 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-03-31 00:52:06.025722 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-03-31 00:52:06.118387 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-03-31 00:52:06.215016 INFO::Writing residuals to file output2/fits/residuals.rds
2026-03-31 00:52:06.277898 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-03-31 00:52:06.338992 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-03-31 00:52:06.344231 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-03-31 00:52:06.348399 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 
 29.982   0.806  30.782

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2123.254 1.009125.826