Build/check report for BioC 3.22 - CHECK results for Maaslin2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4897
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*

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: 2026-04-08 00:55:07 -0400 (Wed, 08 Apr 2026)

EndedAt: 2026-04-08 01:00:36 -0400 (Wed, 08 Apr 2026)

EllapsedTime: 329.4 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 122.539  1.119  125.06
* 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"
2026-04-08 00:57:41.973993 INFO::Writing function arguments to log file
2026-04-08 00:57:42.016535 INFO::Verifying options selected are valid
2026-04-08 00:57:42.050049 INFO::Determining format of input files
2026-04-08 00:57:42.051581 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-08 00:57:42.056564 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-08 00:57:42.057824 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-08 00:57:42.060158 INFO::Filter data based on min abundance and min prevalence
2026-04-08 00:57:42.061034 INFO::Total samples in data: 1595
2026-04-08 00:57:42.061883 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-08 00:57:42.065713 INFO::Total filtered features: 0
2026-04-08 00:57:42.066755 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-08 00:57:42.081132 INFO::Total filtered features with variance filtering: 0
2026-04-08 00:57:42.082365 INFO::Filtered feature names from variance filtering:
2026-04-08 00:57:42.083243 INFO::Running selected normalization method: TSS
2026-04-08 00:57:43.134641 INFO::Bypass z-score application to metadata
2026-04-08 00:57:43.135889 INFO::Running selected transform method: AST
2026-04-08 00:57:43.153306 INFO::Running selected analysis method: LM
2026-04-08 00:57:43.760878 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-08 00:57:44.383053 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-08 00:57:44.562348 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-08 00:57:44.70912 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-08 00:57:44.856265 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-08 00:57:45.014207 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-08 00:57:45.157412 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-08 00:57:45.303103 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-08 00:57:45.421843 WARNING::Fitting problem for feature 8 a warning was issued
2026-04-08 00:57:45.565069 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-08 00:57:45.67413 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-08 00:57:45.873995 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-08 00:57:46.0146 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-08 00:57:46.157609 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-08 00:57:46.609148 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-08 00:57:46.738884 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-08 00:57:46.911289 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-08 00:57:47.068265 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-08 00:57:47.230809 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-08 00:57:47.369516 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-08 00:57:47.518447 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-08 00:57:47.667369 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-08 00:57:47.796347 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-08 00:57:47.932853 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-08 00:57:48.075885 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-08 00:57:48.225015 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-08 00:57:48.370958 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-08 00:57:48.521469 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-08 00:57:48.679897 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-08 00:57:48.818083 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-08 00:57:48.968158 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-08 00:57:49.11107 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-08 00:57:49.262937 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-08 00:57:49.398321 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-08 00:57:49.545788 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-08 00:57:49.691874 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-08 00:57:49.836282 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-08 00:57:49.97013 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-08 00:57:50.127764 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-08 00:57:50.29546 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-08 00:57:50.452877 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-08 00:57:50.602645 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-08 00:57:50.750835 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-08 00:57:50.90548 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-08 00:57:51.04698 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-08 00:57:51.194582 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-08 00:57:51.341972 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-08 00:57:51.476701 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-08 00:57:51.615673 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-08 00:57:51.75975 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-08 00:57:51.92013 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-08 00:57:52.073105 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-08 00:57:52.2252 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-08 00:57:52.388142 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-08 00:57:52.532628 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-08 00:57:52.684905 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-08 00:57:52.843776 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-08 00:57:52.989402 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-08 00:57:53.138799 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-08 00:57:53.295287 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-08 00:57:53.439751 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-08 00:57:53.582089 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-08 00:57:53.717539 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-08 00:57:53.854045 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-08 00:57:54.000143 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-08 00:57:54.141027 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-08 00:57:54.279533 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-08 00:57:54.424664 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-08 00:57:54.56032 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-08 00:57:54.700885 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-08 00:57:54.837485 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-08 00:57:54.981258 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-08 00:57:55.137702 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-08 00:57:55.29361 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-08 00:57:55.442172 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-08 00:57:55.59939 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-08 00:57:55.757842 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-08 00:57:55.900793 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-08 00:57:56.044699 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-08 00:57:56.194833 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-08 00:57:56.338842 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-08 00:57:56.494397 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-08 00:57:56.652017 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-08 00:57:56.796575 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-08 00:57:56.973821 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-08 00:57:57.111926 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-08 00:57:57.24871 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-08 00:57:57.391342 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-08 00:57:57.531861 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-08 00:57:57.670131 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-08 00:57:57.882624 INFO::Counting total values for each feature
2026-04-08 00:57:57.914907 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-08 00:57:58.008575 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-08 00:57:58.104226 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-08 00:57:58.202652 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-08 00:57:58.250655 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-08 00:57:58.277605 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-08 00:57:58.283265 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-08 00:57:58.288722 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"
2026-04-08 00:57:58.303416 INFO::Writing function arguments to log file
2026-04-08 00:57:58.309437 INFO::Verifying options selected are valid
2026-04-08 00:57:58.310499 INFO::Determining format of input files
2026-04-08 00:57:58.311821 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-08 00:57:58.317436 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-08 00:57:58.318551 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-04-08 00:57:58.320239 INFO::Filter data based on min abundance and min prevalence
2026-04-08 00:57:58.321115 INFO::Total samples in data: 1595
2026-04-08 00:57:58.321956 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-08 00:57:58.326212 INFO::Total filtered features: 0
2026-04-08 00:57:58.327245 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-08 00:57:58.334941 INFO::Total filtered features with variance filtering: 0
2026-04-08 00:57:58.336016 INFO::Filtered feature names from variance filtering:
2026-04-08 00:57:58.336875 INFO::Running selected normalization method: NONE
2026-04-08 00:57:58.337693 INFO::Bypass z-score application to metadata
2026-04-08 00:57:58.338516 INFO::Running selected transform method: AST
2026-04-08 00:57:58.354747 INFO::Running selected analysis method: LM
2026-04-08 00:57:58.356591 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-08 00:57:58.503099 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-08 00:57:58.640984 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-08 00:57:58.7765 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-08 00:57:58.919032 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-08 00:57:59.068162 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-08 00:57:59.203936 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-08 00:57:59.341829 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-08 00:57:59.489355 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-08 00:57:59.627519 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-08 00:57:59.766376 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-08 00:57:59.881304 WARNING::Fitting problem for feature 11 a warning was issued
2026-04-08 00:58:00.032715 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-08 00:58:00.161905 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-08 00:58:00.29801 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-08 00:58:00.434746 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-08 00:58:00.584657 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-08 00:58:00.694 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-08 00:58:00.830852 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-08 00:58:00.98041 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-08 00:58:01.111855 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-08 00:58:01.239209 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-08 00:58:01.373326 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-08 00:58:01.512235 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-08 00:58:01.646795 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-08 00:58:01.778179 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-08 00:58:01.922232 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-08 00:58:02.051796 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-08 00:58:02.185541 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-08 00:58:02.336121 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-08 00:58:02.467413 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-08 00:58:02.595541 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-08 00:58:02.74106 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-08 00:58:02.876392 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-08 00:58:03.014662 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-08 00:58:03.155945 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-08 00:58:03.291923 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-08 00:58:03.424942 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-08 00:58:03.566252 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-08 00:58:03.702098 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-08 00:58:03.83947 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-08 00:58:03.975723 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-08 00:58:04.104242 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-08 00:58:04.252551 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-08 00:58:04.38424 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-08 00:58:04.528872 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-08 00:58:04.678898 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-08 00:58:04.81596 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-08 00:58:04.976399 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-08 00:58:05.118051 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-08 00:58:05.266244 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-08 00:58:05.398815 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-08 00:58:05.533241 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-08 00:58:05.668397 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-08 00:58:06.109689 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-08 00:58:06.241763 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-08 00:58:06.371641 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-08 00:58:06.507533 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-08 00:58:06.655381 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-08 00:58:06.789107 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-08 00:58:06.920867 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-08 00:58:07.062837 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-08 00:58:07.204392 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-08 00:58:07.347706 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-08 00:58:07.487304 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-08 00:58:07.626733 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-08 00:58:07.771379 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-08 00:58:07.902845 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-08 00:58:08.043981 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-08 00:58:08.166404 WARNING::Fitting problem for feature 67 a warning was issued
2026-04-08 00:58:08.311734 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-08 00:58:08.445467 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-08 00:58:08.590336 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-08 00:58:08.740334 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-08 00:58:08.887968 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-08 00:58:08.941759 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-08 00:58:09.092867 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-08 00:58:09.247198 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-08 00:58:09.383414 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-08 00:58:09.514646 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-08 00:58:09.6505 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-08 00:58:09.790333 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-08 00:58:09.925654 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-08 00:58:10.064598 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-08 00:58:10.197287 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-08 00:58:10.343885 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-08 00:58:10.472311 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-08 00:58:10.603847 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-08 00:58:10.742123 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-08 00:58:10.873691 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-08 00:58:11.01014 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-08 00:58:11.172391 INFO::Counting total values for each feature
2026-04-08 00:58:11.19974 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-08 00:58:11.292455 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-08 00:58:11.386037 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-08 00:58:11.483402 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-08 00:58:11.546805 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-08 00:58:11.608062 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-08 00:58:11.613419 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-08 00:58:11.617657 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 
 30.173   0.568  30.729

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	122.539	1.119	125.060