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This page was generated on 2025-09-11 12:07 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1149/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.23.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.23.0.tar.gz
StartedAt: 2025-09-09 08:17:25 -0000 (Tue, 09 Sep 2025)
EndedAt: 2025-09-09 08:20:50 -0000 (Tue, 09 Sep 2025)
EllapsedTime: 205.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 122.812  0.893 124.089
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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: aarch64-unknown-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"
2025-09-09 08:20:04.78912 INFO::Writing function arguments to log file
2025-09-09 08:20:04.844428 INFO::Verifying options selected are valid
2025-09-09 08:20:04.8899 INFO::Determining format of input files
2025-09-09 08:20:04.892063 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 08:20:04.900136 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-09 08:20:04.902365 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-09 08:20:04.906248 INFO::Filter data based on min abundance and min prevalence
2025-09-09 08:20:04.907819 INFO::Total samples in data: 1595
2025-09-09 08:20:04.90927 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-09 08:20:04.926781 INFO::Total filtered features: 0
2025-09-09 08:20:04.928642 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-09 08:20:04.956418 INFO::Total filtered features with variance filtering: 0
2025-09-09 08:20:04.95825 INFO::Filtered feature names from variance filtering:
2025-09-09 08:20:04.959707 INFO::Running selected normalization method: TSS
2025-09-09 08:20:06.30494 INFO::Bypass z-score application to metadata
2025-09-09 08:20:06.306552 INFO::Running selected transform method: AST
2025-09-09 08:20:06.327187 INFO::Running selected analysis method: LM
2025-09-09 08:20:07.018347 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-09 08:20:07.68206 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-09 08:20:07.904283 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-09 08:20:08.148009 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-09 08:20:08.368955 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-09 08:20:08.588792 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-09 08:20:08.808011 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-09 08:20:09.043431 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-09 08:20:09.249407 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-09 08:20:09.467837 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-09 08:20:09.70586 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-09 08:20:09.93431 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-09 08:20:10.152682 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-09 08:20:10.369192 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-09 08:20:10.599412 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-09 08:20:10.809576 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-09 08:20:11.027442 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-09 08:20:11.245991 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-09 08:20:11.469059 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-09 08:20:11.706249 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-09 08:20:11.939898 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-09 08:20:12.159723 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-09 08:20:12.374782 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-09 08:20:12.59171 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-09 08:20:12.800114 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-09 08:20:13.015356 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-09 08:20:13.247863 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-09 08:20:13.459018 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-09 08:20:13.677781 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-09 08:20:13.903625 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-09 08:20:14.122215 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-09 08:20:14.355865 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-09 08:20:14.60679 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-09 08:20:14.83645 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-09 08:20:15.068317 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-09 08:20:15.289755 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-09 08:20:15.502876 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-09 08:20:15.72705 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-09 08:20:15.948857 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-09 08:20:16.153884 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-09 08:20:16.371938 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-09 08:20:16.590677 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-09 08:20:16.813695 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-09 08:20:17.041527 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-09 08:20:17.266361 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-09 08:20:17.472114 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-09 08:20:17.685565 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-09 08:20:17.911524 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-09 08:20:18.131902 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-09 08:20:18.3547 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-09 08:20:18.576103 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-09 08:20:18.811181 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-09 08:20:19.022167 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-09 08:20:19.248999 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-09 08:20:19.482172 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-09 08:20:19.690464 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-09 08:20:19.919661 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-09 08:20:20.150327 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-09 08:20:20.386574 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-09 08:20:20.641251 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-09 08:20:20.859108 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-09 08:20:21.080486 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-09 08:20:21.338264 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-09 08:20:21.56464 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-09 08:20:21.785787 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-09 08:20:22.206431 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-09 08:20:22.415267 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-09 08:20:22.625632 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-09 08:20:22.83997 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-09 08:20:23.050622 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-09 08:20:23.271258 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-09 08:20:23.491737 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-09 08:20:23.706434 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-09 08:20:23.921173 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-09 08:20:24.138948 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-09 08:20:24.371459 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-09 08:20:24.594646 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-09 08:20:24.811257 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-09 08:20:25.037179 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-09 08:20:25.264035 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-09 08:20:25.495692 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-09 08:20:25.719923 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-09 08:20:25.938213 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-09 08:20:26.151439 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-09 08:20:26.365157 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-09 08:20:26.576105 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-09 08:20:26.797995 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-09 08:20:27.016061 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-09 08:20:27.285351 INFO::Counting total values for each feature
2025-09-09 08:20:27.340987 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-09 08:20:27.459673 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-09 08:20:27.580586 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-09 08:20:27.704085 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-09 08:20:27.759742 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-09 08:20:27.790291 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-09 08:20:27.796928 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-09 08:20:27.803678 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"
2025-09-09 08:20:27.820986 INFO::Writing function arguments to log file
2025-09-09 08:20:27.829514 INFO::Verifying options selected are valid
2025-09-09 08:20:27.830944 INFO::Determining format of input files
2025-09-09 08:20:27.832664 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 08:20:27.840399 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-09 08:20:27.84226 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-09-09 08:20:27.844526 INFO::Filter data based on min abundance and min prevalence
2025-09-09 08:20:27.845792 INFO::Total samples in data: 1595
2025-09-09 08:20:27.846979 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-09 08:20:27.855462 INFO::Total filtered features: 0
2025-09-09 08:20:27.857107 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-09 08:20:27.883507 INFO::Total filtered features with variance filtering: 0
2025-09-09 08:20:27.885165 INFO::Filtered feature names from variance filtering:
2025-09-09 08:20:27.886365 INFO::Running selected normalization method: NONE
2025-09-09 08:20:27.887513 INFO::Bypass z-score application to metadata
2025-09-09 08:20:27.888682 INFO::Running selected transform method: AST
2025-09-09 08:20:27.91649 INFO::Running selected analysis method: LM
2025-09-09 08:20:27.918547 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-09 08:20:28.120047 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-09 08:20:28.357327 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-09 08:20:28.568913 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-09 08:20:28.789464 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-09 08:20:29.005784 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-09 08:20:29.219912 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-09 08:20:29.449141 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-09 08:20:29.668546 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-09 08:20:29.836159 WARNING::Fitting problem for feature 9 a warning was issued
2025-09-09 08:20:30.064029 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-09 08:20:30.299763 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-09 08:20:30.508551 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-09 08:20:30.70664 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-09 08:20:30.891213 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-09 08:20:31.108276 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-09 08:20:31.326254 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-09 08:20:31.56566 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-09 08:20:31.730113 WARNING::Fitting problem for feature 16 a warning was issued
2025-09-09 08:20:31.948541 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-09 08:20:32.171291 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-09 08:20:32.372442 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-09 08:20:32.571827 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-09 08:20:32.783851 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-09 08:20:32.990742 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-09 08:20:33.212567 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-09 08:20:33.409635 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-09 08:20:33.642213 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-09 08:20:33.846274 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-09 08:20:34.049279 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-09 08:20:34.265855 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-09 08:20:34.458707 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-09 08:20:34.654245 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-09 08:20:34.867561 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-09 08:20:35.06851 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-09 08:20:35.279088 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-09 08:20:35.49806 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-09 08:20:35.702739 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-09 08:20:35.905796 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-09 08:20:36.118912 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-09 08:20:36.318668 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-09 08:20:36.522737 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-09 08:20:36.733335 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-09 08:20:36.930134 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-09 08:20:37.148403 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-09 08:20:37.348307 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-09 08:20:37.553708 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-09 08:20:37.77124 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-09 08:20:37.974612 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-09 08:20:38.184152 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-09 08:20:38.394103 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-09 08:20:38.623963 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-09 08:20:38.842531 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-09 08:20:39.055419 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-09 08:20:39.263554 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-09 08:20:39.469939 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-09 08:20:39.663325 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-09 08:20:39.860414 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-09 08:20:40.072294 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-09 08:20:40.275374 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-09 08:20:40.489073 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-09 08:20:40.690812 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-09 08:20:40.91297 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-09 08:20:41.110983 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-09 08:20:41.325843 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-09 08:20:41.520398 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-09 08:20:41.734652 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-09 08:20:41.938298 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-09 08:20:42.158734 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-09 08:20:42.358211 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-09 08:20:42.578852 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-09 08:20:42.783453 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-09 08:20:42.994834 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-09 08:20:43.434703 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-09 08:20:43.641564 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-09 08:20:43.712316 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-09 08:20:43.919985 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-09 08:20:44.139059 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-09 08:20:44.343327 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-09 08:20:44.556302 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-09 08:20:44.778769 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-09 08:20:44.99164 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-09 08:20:45.216487 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-09 08:20:45.429103 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-09 08:20:45.630742 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-09 08:20:45.844635 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-09 08:20:46.054577 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-09 08:20:46.25434 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-09 08:20:46.452993 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-09 08:20:46.653212 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-09 08:20:46.876185 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-09 08:20:47.109514 INFO::Counting total values for each feature
2025-09-09 08:20:47.14209 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-09 08:20:47.258845 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-09 08:20:47.376029 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-09 08:20:47.498502 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-09 08:20:47.572848 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-09 08:20:47.643643 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-09 08:20:47.650324 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-09 08:20:47.656031 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 43.623   0.586  44.327

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2122.812 0.893124.089