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This page was generated on 2025-10-06 11:41 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 1154/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.22.0  (landing page)
Lauren McIver
Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_21
git_last_commit: fcec85e
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Maaslin2 on kunpeng2

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: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2025-10-03 10:51:52 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 10:55:22 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 209.2 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* 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 123.015  1.101  124.46
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.22.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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"
2025-10-03 10:54:33.352079 INFO::Writing function arguments to log file
2025-10-03 10:54:33.409573 INFO::Verifying options selected are valid
2025-10-03 10:54:33.455223 INFO::Determining format of input files
2025-10-03 10:54:33.457365 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-03 10:54:33.465501 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-10-03 10:54:33.467524 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-10-03 10:54:33.471161 INFO::Filter data based on min abundance and min prevalence
2025-10-03 10:54:33.472597 INFO::Total samples in data: 1595
2025-10-03 10:54:33.473881 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-10-03 10:54:33.483933 INFO::Total filtered features: 0
2025-10-03 10:54:33.495201 INFO::Filtered feature names from abundance and prevalence filtering:
2025-10-03 10:54:33.523101 INFO::Total filtered features with variance filtering: 0
2025-10-03 10:54:33.524843 INFO::Filtered feature names from variance filtering:
2025-10-03 10:54:33.526311 INFO::Running selected normalization method: TSS
2025-10-03 10:54:35.059045 INFO::Bypass z-score application to metadata
2025-10-03 10:54:35.060652 INFO::Running selected transform method: AST
2025-10-03 10:54:35.084868 INFO::Running selected analysis method: LM
2025-10-03 10:54:35.782634 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-10-03 10:54:36.290042 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-10-03 10:54:36.529799 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-10-03 10:54:36.771544 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-10-03 10:54:37.028343 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-10-03 10:54:37.262208 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-10-03 10:54:37.495844 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-10-03 10:54:37.737993 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-10-03 10:54:37.974098 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-10-03 10:54:38.211299 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-10-03 10:54:38.465732 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-10-03 10:54:38.725039 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-10-03 10:54:38.954125 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-10-03 10:54:39.146698 WARNING::Fitting problem for feature 13 a warning was issued
2025-10-03 10:54:39.446509 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-10-03 10:54:39.675071 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-10-03 10:54:39.905356 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-10-03 10:54:40.138842 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-10-03 10:54:40.378986 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-10-03 10:54:40.611556 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-10-03 10:54:41.140607 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-10-03 10:54:41.377849 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-10-03 10:54:41.613668 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-10-03 10:54:41.838922 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-10-03 10:54:42.074826 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-10-03 10:54:42.316568 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-10-03 10:54:42.544465 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-10-03 10:54:42.77087 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-10-03 10:54:43.031312 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-10-03 10:54:43.273836 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-10-03 10:54:43.541204 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-10-03 10:54:43.765055 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-10-03 10:54:44.000097 INFO::Fitting model to feature number 32, Prevotella.copri
2025-10-03 10:54:44.226328 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-10-03 10:54:44.474078 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-10-03 10:54:44.694908 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-10-03 10:54:44.920761 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-10-03 10:54:45.156149 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-10-03 10:54:45.383121 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-10-03 10:54:45.604591 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-10-03 10:54:45.850891 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-10-03 10:54:46.098025 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-10-03 10:54:46.351791 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-10-03 10:54:46.601455 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-10-03 10:54:46.817928 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-10-03 10:54:47.029703 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-10-03 10:54:47.257523 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-10-03 10:54:47.480767 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-10-03 10:54:47.710345 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-10-03 10:54:47.936206 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-10-03 10:54:48.157204 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-10-03 10:54:48.385388 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-10-03 10:54:48.602121 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-10-03 10:54:48.825798 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-10-03 10:54:49.07164 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-10-03 10:54:49.314866 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-10-03 10:54:49.56949 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-10-03 10:54:49.811133 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-10-03 10:54:50.026645 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-10-03 10:54:50.264345 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-10-03 10:54:50.479993 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-10-03 10:54:50.705064 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-10-03 10:54:50.927827 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-10-03 10:54:51.168456 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-10-03 10:54:51.390849 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-10-03 10:54:51.616466 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-10-03 10:54:51.833753 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-10-03 10:54:52.067578 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-10-03 10:54:52.281478 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-10-03 10:54:52.523352 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-10-03 10:54:52.779474 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-10-03 10:54:53.033661 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-10-03 10:54:53.267054 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-10-03 10:54:53.488282 INFO::Fitting model to feature number 73, Dialister.invisus
2025-10-03 10:54:54.025945 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-10-03 10:54:54.253907 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-10-03 10:54:54.488454 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-10-03 10:54:54.718023 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-10-03 10:54:54.963553 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-10-03 10:54:55.219508 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-10-03 10:54:55.456688 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-10-03 10:54:55.684138 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-10-03 10:54:55.931563 INFO::Fitting model to feature number 82, Escherichia.coli
2025-10-03 10:54:56.163586 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-10-03 10:54:56.381445 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-10-03 10:54:56.610185 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-10-03 10:54:56.847494 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-10-03 10:54:57.086848 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-10-03 10:54:57.402928 INFO::Counting total values for each feature
2025-10-03 10:54:57.45859 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-10-03 10:54:57.57552 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-10-03 10:54:57.694423 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-10-03 10:54:57.817174 INFO::Writing residuals to file output/fits/residuals.rds
2025-10-03 10:54:57.874109 INFO::Writing fitted values to file output/fits/fitted.rds
2025-10-03 10:54:57.905668 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-10-03 10:54:58.230141 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-10-03 10:54:58.237783 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"
2025-10-03 10:54:58.254808 INFO::Writing function arguments to log file
2025-10-03 10:54:58.262978 INFO::Verifying options selected are valid
2025-10-03 10:54:58.264382 INFO::Determining format of input files
2025-10-03 10:54:58.266114 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-03 10:54:58.274187 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-10-03 10:54:58.275904 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-10-03 10:54:58.278301 INFO::Filter data based on min abundance and min prevalence
2025-10-03 10:54:58.279603 INFO::Total samples in data: 1595
2025-10-03 10:54:58.280853 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-10-03 10:54:58.29033 INFO::Total filtered features: 0
2025-10-03 10:54:58.291944 INFO::Filtered feature names from abundance and prevalence filtering:
2025-10-03 10:54:58.319174 INFO::Total filtered features with variance filtering: 0
2025-10-03 10:54:58.320819 INFO::Filtered feature names from variance filtering:
2025-10-03 10:54:58.322105 INFO::Running selected normalization method: NONE
2025-10-03 10:54:58.323295 INFO::Bypass z-score application to metadata
2025-10-03 10:54:58.32448 INFO::Running selected transform method: AST
2025-10-03 10:54:58.34743 INFO::Running selected analysis method: LM
2025-10-03 10:54:58.349524 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-10-03 10:54:58.566902 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-10-03 10:54:58.784421 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-10-03 10:54:58.996874 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-10-03 10:54:59.229499 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-10-03 10:54:59.4483 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-10-03 10:54:59.683905 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-10-03 10:54:59.917785 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-10-03 10:55:00.15065 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-10-03 10:55:00.339604 WARNING::Fitting problem for feature 9 a warning was issued
2025-10-03 10:55:00.603836 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-10-03 10:55:00.825297 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-10-03 10:55:01.057687 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-10-03 10:55:01.269164 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-10-03 10:55:01.449282 WARNING::Fitting problem for feature 13 a warning was issued
2025-10-03 10:55:01.677207 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-10-03 10:55:01.904294 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-10-03 10:55:02.157064 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-10-03 10:55:02.337534 WARNING::Fitting problem for feature 16 a warning was issued
2025-10-03 10:55:02.56588 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-10-03 10:55:02.791013 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-10-03 10:55:03.025202 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-10-03 10:55:03.248711 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-10-03 10:55:03.461318 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-10-03 10:55:03.679194 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-10-03 10:55:03.910134 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-10-03 10:55:04.117807 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-10-03 10:55:04.335074 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-10-03 10:55:04.553925 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-10-03 10:55:04.781539 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-10-03 10:55:05.001067 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-10-03 10:55:05.21628 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-10-03 10:55:05.428723 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-10-03 10:55:05.642022 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-10-03 10:55:05.878545 INFO::Fitting model to feature number 32, Prevotella.copri
2025-10-03 10:55:06.114767 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-10-03 10:55:06.329178 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-10-03 10:55:06.549606 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-10-03 10:55:06.773067 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-10-03 10:55:06.992225 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-10-03 10:55:07.20683 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-10-03 10:55:07.422226 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-10-03 10:55:07.669818 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-10-03 10:55:07.882014 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-10-03 10:55:08.103358 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-10-03 10:55:08.327393 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-10-03 10:55:08.564726 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-10-03 10:55:08.78544 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-10-03 10:55:09.00143 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-10-03 10:55:09.227808 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-10-03 10:55:09.453084 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-10-03 10:55:09.673244 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-10-03 10:55:09.889022 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-10-03 10:55:10.09852 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-10-03 10:55:10.338212 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-10-03 10:55:10.542817 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-10-03 10:55:10.743314 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-10-03 10:55:10.951289 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-10-03 10:55:11.172328 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-10-03 10:55:11.388677 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-10-03 10:55:11.600661 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-10-03 10:55:11.812727 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-10-03 10:55:12.04121 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-10-03 10:55:12.254869 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-10-03 10:55:12.470033 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-10-03 10:55:12.689448 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-10-03 10:55:12.90061 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-10-03 10:55:13.110024 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-10-03 10:55:13.320247 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-10-03 10:55:13.554619 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-10-03 10:55:13.782328 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-10-03 10:55:14.003946 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-10-03 10:55:14.563074 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-10-03 10:55:14.798387 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-10-03 10:55:15.016292 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-10-03 10:55:15.090233 WARNING::Fitting problem for feature 72 a warning was issued
2025-10-03 10:55:15.301056 INFO::Fitting model to feature number 73, Dialister.invisus
2025-10-03 10:55:15.529124 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-10-03 10:55:15.748156 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-10-03 10:55:15.96632 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-10-03 10:55:16.184408 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-10-03 10:55:16.408397 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-10-03 10:55:16.625731 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-10-03 10:55:16.852118 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-10-03 10:55:17.065433 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-10-03 10:55:17.300084 INFO::Fitting model to feature number 82, Escherichia.coli
2025-10-03 10:55:17.517936 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-10-03 10:55:17.73096 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-10-03 10:55:17.94763 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-10-03 10:55:18.185122 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-10-03 10:55:18.406489 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-10-03 10:55:18.668553 INFO::Counting total values for each feature
2025-10-03 10:55:18.706234 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-10-03 10:55:18.822235 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-10-03 10:55:18.938063 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-10-03 10:55:19.06038 INFO::Writing residuals to file output2/fits/residuals.rds
2025-10-03 10:55:19.135478 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-10-03 10:55:19.207217 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-10-03 10:55:19.214027 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-10-03 10:55:19.219824 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 
 46.828   0.522  47.447 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2123.015 1.101124.460