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This page was generated on 2025-08-25 12:06 -0400 (Mon, 25 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1147/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-08-24 13:45 -0400 (Sun, 24 Aug 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 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: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2025-08-24 20:06:05 -0400 (Sun, 24 Aug 2025)
EndedAt: 2025-08-24 20:07:05 -0400 (Sun, 24 Aug 2025)
EllapsedTime: 59.8 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 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 30.107  0.616  31.298
* 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-3.22-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/4.5-arm64/Resources/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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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"
2025-08-24 20:06:51.310387 INFO::Writing function arguments to log file
2025-08-24 20:06:51.328047 INFO::Verifying options selected are valid
2025-08-24 20:06:51.341818 INFO::Determining format of input files
2025-08-24 20:06:51.342438 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-24 20:06:51.344496 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-24 20:06:51.344964 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-24 20:06:51.345761 INFO::Filter data based on min abundance and min prevalence
2025-08-24 20:06:51.34606 INFO::Total samples in data: 1595
2025-08-24 20:06:51.346339 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-24 20:06:51.3512 INFO::Total filtered features: 0
2025-08-24 20:06:51.351659 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-24 20:06:51.354705 INFO::Total filtered features with variance filtering: 0
2025-08-24 20:06:51.355065 INFO::Filtered feature names from variance filtering:
2025-08-24 20:06:51.368598 INFO::Running selected normalization method: TSS
2025-08-24 20:06:51.776379 INFO::Bypass z-score application to metadata
2025-08-24 20:06:51.776882 INFO::Running selected transform method: AST
2025-08-24 20:06:51.78267 INFO::Running selected analysis method: LM
2025-08-24 20:06:52.009688 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-24 20:06:52.169801 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-24 20:06:52.22222 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-24 20:06:52.284494 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-24 20:06:52.338132 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-24 20:06:52.392845 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-24 20:06:52.445971 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-24 20:06:52.499734 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-24 20:06:52.543758 WARNING::Fitting problem for feature 8 a warning was issued
2025-08-24 20:06:52.598178 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-24 20:06:52.645803 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-24 20:06:52.701411 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-24 20:06:52.75246 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-24 20:06:52.821027 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-24 20:06:52.871919 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-24 20:06:52.924538 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-24 20:06:52.97607 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-24 20:06:53.03199 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-24 20:06:53.082471 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-24 20:06:53.135069 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-24 20:06:53.191312 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-24 20:06:53.239498 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-24 20:06:53.29081 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-24 20:06:53.4543 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-24 20:06:53.509647 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-24 20:06:53.561582 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-24 20:06:53.618172 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-24 20:06:53.676653 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-24 20:06:53.724792 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-24 20:06:53.77842 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-24 20:06:53.833442 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-24 20:06:53.886141 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-24 20:06:53.937035 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-24 20:06:53.997202 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-24 20:06:54.051197 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-24 20:06:54.103963 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-24 20:06:54.156837 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-24 20:06:54.205203 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-24 20:06:54.255909 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-24 20:06:54.311885 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-24 20:06:54.359822 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-24 20:06:54.410466 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-24 20:06:54.469045 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-24 20:06:54.519636 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-24 20:06:54.573577 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-24 20:06:54.629112 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-24 20:06:54.675962 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-24 20:06:54.726436 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-24 20:06:54.78199 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-24 20:06:54.835261 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-24 20:06:54.884579 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-24 20:06:54.936893 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-24 20:06:54.985067 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-24 20:06:55.037892 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-24 20:06:55.089659 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-24 20:06:55.146257 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-24 20:06:55.201206 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-24 20:06:55.252225 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-24 20:06:55.308766 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-24 20:06:55.354638 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-24 20:06:55.407127 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-24 20:06:55.456794 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-24 20:06:55.510781 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-24 20:06:55.5622 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-24 20:06:55.616816 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-24 20:06:55.668187 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-24 20:06:55.722394 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-24 20:06:55.771038 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-24 20:06:55.825867 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-24 20:06:55.876558 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-24 20:06:55.927011 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-24 20:06:55.987697 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-24 20:06:56.039375 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-24 20:06:56.089363 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-24 20:06:56.14394 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-24 20:06:56.194063 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-24 20:06:56.244491 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-24 20:06:56.301711 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-24 20:06:56.351691 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-24 20:06:56.39986 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-24 20:06:56.457009 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-24 20:06:56.509711 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-24 20:06:56.560711 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-24 20:06:56.619091 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-24 20:06:56.670389 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-24 20:06:56.718723 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-24 20:06:56.772551 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-24 20:06:56.82091 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-24 20:06:56.870974 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-24 20:06:56.941751 INFO::Counting total values for each feature
2025-08-24 20:06:56.954557 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-24 20:06:57.00444 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-24 20:06:57.062678 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-24 20:06:57.128769 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-24 20:06:57.15567 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-24 20:06:57.17062 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-24 20:06:57.173771 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-24 20:06:57.177019 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"
2025-08-24 20:06:57.182357 INFO::Writing function arguments to log file
2025-08-24 20:06:57.184785 INFO::Verifying options selected are valid
2025-08-24 20:06:57.185323 INFO::Determining format of input files
2025-08-24 20:06:57.185793 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-24 20:06:57.18793 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-24 20:06:57.188294 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-24 20:06:57.188842 INFO::Filter data based on min abundance and min prevalence
2025-08-24 20:06:57.189123 INFO::Total samples in data: 1595
2025-08-24 20:06:57.18938 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-24 20:06:57.190935 INFO::Total filtered features: 0
2025-08-24 20:06:57.191245 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-24 20:06:57.194352 INFO::Total filtered features with variance filtering: 0
2025-08-24 20:06:57.194878 INFO::Filtered feature names from variance filtering:
2025-08-24 20:06:57.195255 INFO::Running selected normalization method: NONE
2025-08-24 20:06:57.195533 INFO::Bypass z-score application to metadata
2025-08-24 20:06:57.195795 INFO::Running selected transform method: AST
2025-08-24 20:06:57.20431 INFO::Running selected analysis method: LM
2025-08-24 20:06:57.20529 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-24 20:06:57.258165 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-24 20:06:57.316737 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-24 20:06:57.367456 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-24 20:06:57.53101 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-24 20:06:57.581076 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-24 20:06:57.637653 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-24 20:06:57.692876 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-24 20:06:57.746479 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-24 20:06:57.787514 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-24 20:06:57.841214 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-24 20:06:57.899652 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-24 20:06:57.952841 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-24 20:06:58.003257 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-24 20:06:58.046328 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-24 20:06:58.103971 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-24 20:06:58.15233 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-24 20:06:58.202482 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-24 20:06:58.241918 WARNING::Fitting problem for feature 16 a warning was issued
2025-08-24 20:06:58.294452 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-24 20:06:58.345204 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-24 20:06:58.396728 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-24 20:06:58.4497 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-24 20:06:58.4984 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-24 20:06:58.55122 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-24 20:06:58.602366 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-24 20:06:58.654963 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-24 20:06:58.706168 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-24 20:06:58.755453 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-24 20:06:58.808586 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-24 20:06:58.857922 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-24 20:06:58.904646 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-24 20:06:58.954993 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-24 20:06:59.003018 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-24 20:06:59.052219 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-24 20:06:59.108258 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-24 20:06:59.156812 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-24 20:06:59.205163 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-24 20:06:59.256108 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-24 20:06:59.304437 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-24 20:06:59.353673 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-24 20:06:59.407219 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-24 20:06:59.456162 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-24 20:06:59.504475 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-24 20:06:59.559404 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-24 20:06:59.609777 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-24 20:06:59.662763 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-24 20:06:59.721568 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-24 20:06:59.76981 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-24 20:06:59.821099 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-24 20:06:59.868355 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-24 20:06:59.922213 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-24 20:06:59.96992 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-24 20:07:00.016215 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-24 20:07:00.073908 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-24 20:07:00.119516 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-24 20:07:00.166628 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-24 20:07:00.216756 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-24 20:07:00.271628 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-24 20:07:00.320294 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-24 20:07:00.369132 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-24 20:07:00.423097 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-24 20:07:00.473524 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-24 20:07:00.521942 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-24 20:07:00.575809 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-24 20:07:00.624503 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-24 20:07:00.673976 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-24 20:07:00.72804 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-24 20:07:00.776785 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-24 20:07:00.826592 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-24 20:07:00.885243 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-24 20:07:00.93468 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-24 20:07:00.987629 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-24 20:07:01.044786 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-24 20:07:01.093157 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-24 20:07:01.111558 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-24 20:07:01.168113 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-24 20:07:01.218453 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-24 20:07:01.269446 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-24 20:07:01.323176 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-24 20:07:01.374929 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-24 20:07:01.430697 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-24 20:07:01.479307 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-24 20:07:01.534497 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-24 20:07:01.583285 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-24 20:07:01.636506 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-24 20:07:01.690825 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-24 20:07:01.737644 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-24 20:07:01.78898 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-24 20:07:01.837228 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-24 20:07:01.893358 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-24 20:07:01.955096 INFO::Counting total values for each feature
2025-08-24 20:07:01.963453 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-24 20:07:02.013188 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-24 20:07:02.06256 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-24 20:07:02.12092 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-24 20:07:02.157062 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-24 20:07:02.191969 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-24 20:07:02.195028 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-24 20:07:02.197409 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 11.020   0.279  11.325

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin230.107 0.61631.298