Multiple platform build/check report for BioC 3.23 - CHECK results for Maaslin2 on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4990
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4723
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 kjohnson3

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: 1.26.0

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_1.26.0.tar.gz

StartedAt: 2026-05-06 20:58:37 -0400 (Wed, 06 May 2026)

EndedAt: 2026-05-06 20:59:49 -0400 (Wed, 06 May 2026)

EllapsedTime: 71.9 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-07 00:58:37 UTC
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.26.0’
* 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: 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 40.266  0.606  41.877
* 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-3.23-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/4.6/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.26.0’
** 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 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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"
2026-05-06 20:59:35.035902 INFO::Writing function arguments to log file
2026-05-06 20:59:35.047803 INFO::Verifying options selected are valid
2026-05-06 20:59:35.061764 INFO::Determining format of input files
2026-05-06 20:59:35.062628 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-06 20:59:35.06522 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-06 20:59:35.067909 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-06 20:59:35.072514 INFO::Filter data based on min abundance and min prevalence
2026-05-06 20:59:35.07322 INFO::Total samples in data: 1595
2026-05-06 20:59:35.07368 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-06 20:59:35.075341 INFO::Total filtered features: 0
2026-05-06 20:59:35.075891 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-06 20:59:35.079043 INFO::Total filtered features with variance filtering: 0
2026-05-06 20:59:35.079577 INFO::Filtered feature names from variance filtering:
2026-05-06 20:59:35.080028 INFO::Running selected normalization method: TSS
2026-05-06 20:59:35.489538 INFO::Bypass z-score application to metadata
2026-05-06 20:59:35.490282 INFO::Running selected transform method: AST
2026-05-06 20:59:35.500291 INFO::Running selected analysis method: LM
2026-05-06 20:59:35.766604 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-06 20:59:36.007797 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-06 20:59:36.076693 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-06 20:59:36.133014 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-06 20:59:36.188601 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-06 20:59:36.249762 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-06 20:59:36.304172 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-06 20:59:36.36055 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-06 20:59:36.416585 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-06 20:59:36.465616 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-06 20:59:36.517666 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-06 20:59:36.592179 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-06 20:59:36.641409 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-06 20:59:36.693695 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-06 20:59:36.745944 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-06 20:59:36.804227 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-06 20:59:36.855208 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-06 20:59:36.91168 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-06 20:59:36.97013 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-06 20:59:37.021415 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-06 20:59:37.071742 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-06 20:59:37.128937 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-06 20:59:37.183395 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-06 20:59:37.233822 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-06 20:59:37.292827 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-06 20:59:37.345814 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-06 20:59:37.396233 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-06 20:59:37.456061 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-06 20:59:37.51124 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-06 20:59:37.567492 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-06 20:59:37.628451 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-06 20:59:37.684482 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-06 20:59:37.737699 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-06 20:59:37.796987 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-06 20:59:37.846425 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-06 20:59:37.904454 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-06 20:59:37.956074 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-06 20:59:38.00993 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-06 20:59:38.063856 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-06 20:59:38.112563 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-06 20:59:38.172679 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-06 20:59:38.221686 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-06 20:59:38.274892 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-06 20:59:38.331238 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-06 20:59:38.390945 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-06 20:59:38.443686 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-06 20:59:38.49977 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-06 20:59:38.555362 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-06 20:59:38.60691 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-06 20:59:38.667753 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-06 20:59:38.716742 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-06 20:59:38.767143 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-06 20:59:38.82086 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-06 20:59:38.873438 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-06 20:59:38.920329 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-06 20:59:38.977804 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-06 20:59:39.0346 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-06 20:59:39.091419 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-06 20:59:39.147003 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-06 20:59:39.199739 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-06 20:59:39.256743 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-06 20:59:39.311238 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-06 20:59:39.368645 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-06 20:59:39.420269 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-06 20:59:39.469553 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-06 20:59:39.5232 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-06 20:59:39.574777 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-06 20:59:39.628526 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-06 20:59:39.680133 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-06 20:59:39.740897 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-06 20:59:39.795272 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-06 20:59:39.953788 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-06 20:59:40.007373 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-06 20:59:40.057653 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-06 20:59:40.108765 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-06 20:59:40.164402 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-06 20:59:40.21631 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-06 20:59:40.268368 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-06 20:59:40.331291 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-06 20:59:40.389831 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-06 20:59:40.446184 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-06 20:59:40.502906 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-06 20:59:40.559333 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-06 20:59:40.610762 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-06 20:59:40.663927 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-06 20:59:40.719372 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-06 20:59:40.771667 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-06 20:59:40.839603 INFO::Counting total values for each feature
2026-05-06 20:59:40.851546 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-06 20:59:40.898376 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-06 20:59:40.955488 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-06 20:59:41.011315 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-06 20:59:41.038443 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-06 20:59:41.052177 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-06 20:59:41.055255 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-06 20:59:41.062486 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"
2026-05-06 20:59:41.068617 INFO::Writing function arguments to log file
2026-05-06 20:59:41.071952 INFO::Verifying options selected are valid
2026-05-06 20:59:41.072375 INFO::Determining format of input files
2026-05-06 20:59:41.072877 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-06 20:59:41.075088 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-06 20:59:41.075533 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2026-05-06 20:59:41.076161 INFO::Filter data based on min abundance and min prevalence
2026-05-06 20:59:41.076529 INFO::Total samples in data: 1595
2026-05-06 20:59:41.076888 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-06 20:59:41.078316 INFO::Total filtered features: 0
2026-05-06 20:59:41.078713 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-06 20:59:41.081229 INFO::Total filtered features with variance filtering: 0
2026-05-06 20:59:41.081683 INFO::Filtered feature names from variance filtering:
2026-05-06 20:59:41.082094 INFO::Running selected normalization method: NONE
2026-05-06 20:59:41.082446 INFO::Bypass z-score application to metadata
2026-05-06 20:59:41.082826 INFO::Running selected transform method: AST
2026-05-06 20:59:41.088173 INFO::Running selected analysis method: LM
2026-05-06 20:59:41.088811 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-06 20:59:41.136502 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-06 20:59:41.186414 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-06 20:59:41.236342 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-06 20:59:41.284319 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-06 20:59:41.333577 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-06 20:59:41.387713 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-06 20:59:41.440696 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-06 20:59:41.491861 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-06 20:59:41.546203 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-06 20:59:41.605075 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-06 20:59:41.656248 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-06 20:59:41.704897 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-06 20:59:41.753824 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-06 20:59:41.805591 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-06 20:59:41.856631 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-06 20:59:41.904961 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-06 20:59:41.960046 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-06 20:59:42.009552 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-06 20:59:42.05622 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-06 20:59:42.105208 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-06 20:59:42.158521 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-06 20:59:42.208607 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-06 20:59:42.256627 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-06 20:59:42.308001 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-06 20:59:42.359601 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-06 20:59:42.407681 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-06 20:59:42.459374 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-06 20:59:42.514286 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-06 20:59:42.562229 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-06 20:59:42.614139 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-06 20:59:42.667855 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-06 20:59:42.726874 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-06 20:59:42.777769 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-06 20:59:42.828278 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-06 20:59:42.880014 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-06 20:59:42.930769 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-06 20:59:42.985372 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-06 20:59:43.039354 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-06 20:59:43.084648 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-06 20:59:43.131537 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-06 20:59:43.183897 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-06 20:59:43.230773 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-06 20:59:43.282378 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-06 20:59:43.337856 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-06 20:59:43.388416 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-06 20:59:43.439865 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-06 20:59:43.492948 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-06 20:59:43.542636 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-06 20:59:43.593268 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-06 20:59:43.636273 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-06 20:59:43.683658 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-06 20:59:43.737211 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-06 20:59:43.780358 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-06 20:59:43.827304 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-06 20:59:43.877541 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-06 20:59:43.934072 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-06 20:59:43.984392 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-06 20:59:44.033619 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-06 20:59:44.089753 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-06 20:59:44.139071 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-06 20:59:44.190599 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-06 20:59:44.241737 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-06 20:59:44.29826 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-06 20:59:44.347145 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-06 20:59:44.395384 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-06 20:59:44.44448 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-06 20:59:44.497553 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-06 20:59:44.545775 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-06 20:59:44.599529 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-06 20:59:44.652854 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-06 20:59:44.708353 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-06 20:59:44.726167 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-06 20:59:44.777554 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-06 20:59:44.826171 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-06 20:59:44.878463 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-06 20:59:44.925867 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-06 20:59:44.975045 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-06 20:59:45.026185 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-06 20:59:45.081943 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-06 20:59:45.131967 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-06 20:59:45.179384 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-06 20:59:45.235976 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-06 20:59:45.283154 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-06 20:59:45.332658 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-06 20:59:45.383723 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-06 20:59:45.437995 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-06 20:59:45.490144 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-06 20:59:45.550439 INFO::Counting total values for each feature
2026-05-06 20:59:45.563092 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-06 20:59:45.609862 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-06 20:59:45.656131 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-06 20:59:45.711243 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-06 20:59:45.74772 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-06 20:59:45.781962 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-06 20:59:45.785124 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-06 20:59:45.787474 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 1 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 10.996   0.219  11.232

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	40.266	0.606	41.877