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This page was generated on 2025-06-13 12:08 -0400 (Fri, 13 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4797
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4538
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4571
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4515
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4483
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 1142/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-06-12 13:25 -0400 (Thu, 12 Jun 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 lconway

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: 2025-06-12 21:37:50 -0400 (Thu, 12 Jun 2025)
EndedAt: 2025-06-12 21:40:48 -0400 (Thu, 12 Jun 2025)
EllapsedTime: 178.4 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 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 97.115  1.873  99.831
* 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-x86_64/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 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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"
2025-06-12 21:40:08.287248 INFO::Writing function arguments to log file
2025-06-12 21:40:08.336397 INFO::Verifying options selected are valid
2025-06-12 21:40:08.377008 INFO::Determining format of input files
2025-06-12 21:40:08.379479 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-12 21:40:08.387423 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-06-12 21:40:08.389375 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-06-12 21:40:08.392596 INFO::Filter data based on min abundance and min prevalence
2025-06-12 21:40:08.394083 INFO::Total samples in data: 1595
2025-06-12 21:40:08.395475 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-06-12 21:40:08.41047 INFO::Total filtered features: 0
2025-06-12 21:40:08.412173 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-12 21:40:08.422091 INFO::Total filtered features with variance filtering: 0
2025-06-12 21:40:08.423951 INFO::Filtered feature names from variance filtering:
2025-06-12 21:40:08.425249 INFO::Running selected normalization method: TSS
2025-06-12 21:40:09.584211 INFO::Bypass z-score application to metadata
2025-06-12 21:40:09.585467 INFO::Running selected transform method: AST
2025-06-12 21:40:09.601679 INFO::Running selected analysis method: LM
2025-06-12 21:40:10.228831 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-06-12 21:40:10.770487 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-06-12 21:40:10.924466 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-06-12 21:40:11.104024 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-06-12 21:40:11.273599 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-06-12 21:40:11.429282 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-06-12 21:40:11.585821 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-06-12 21:40:11.73777 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-06-12 21:40:11.891171 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-06-12 21:40:12.054446 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-06-12 21:40:12.229616 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-06-12 21:40:12.394177 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-06-12 21:40:12.569356 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-06-12 21:40:12.741971 WARNING::Fitting problem for feature 13 a warning was issued
2025-06-12 21:40:12.899285 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-06-12 21:40:13.065268 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-06-12 21:40:13.237984 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-06-12 21:40:13.393876 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-06-12 21:40:13.53728 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-06-12 21:40:13.705005 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-06-12 21:40:13.865027 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-06-12 21:40:14.005283 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-06-12 21:40:14.163603 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-06-12 21:40:14.33082 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-06-12 21:40:14.478301 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-06-12 21:40:14.629211 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-06-12 21:40:14.80686 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-06-12 21:40:14.968315 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-06-12 21:40:15.132873 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-06-12 21:40:15.300797 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-06-12 21:40:15.457154 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-06-12 21:40:15.60736 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-06-12 21:40:15.78707 INFO::Fitting model to feature number 32, Prevotella.copri
2025-06-12 21:40:15.952419 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-06-12 21:40:16.119108 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-06-12 21:40:16.280241 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-06-12 21:40:16.446486 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-06-12 21:40:16.615163 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-06-12 21:40:16.778168 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-06-12 21:40:16.935132 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-06-12 21:40:17.097939 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-06-12 21:40:17.280733 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-06-12 21:40:17.477173 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-06-12 21:40:17.628717 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-06-12 21:40:17.796609 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-06-12 21:40:17.962437 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-06-12 21:40:18.135878 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-06-12 21:40:18.298238 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-06-12 21:40:18.486806 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-06-12 21:40:18.658818 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-06-12 21:40:18.832393 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-06-12 21:40:19.007201 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-06-12 21:40:19.184481 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-06-12 21:40:19.349428 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-06-12 21:40:19.515989 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-06-12 21:40:19.690161 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-06-12 21:40:19.847358 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-06-12 21:40:20.016462 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-06-12 21:40:20.187335 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-06-12 21:40:20.360669 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-06-12 21:40:20.523959 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-06-12 21:40:20.694465 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-06-12 21:40:20.867894 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-06-12 21:40:21.032441 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-06-12 21:40:21.197508 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-06-12 21:40:21.354712 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-06-12 21:40:21.538473 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-06-12 21:40:21.70192 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-06-12 21:40:21.849786 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-06-12 21:40:22.014457 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-06-12 21:40:22.178443 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-06-12 21:40:22.34296 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-06-12 21:40:22.495 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-06-12 21:40:22.669975 INFO::Fitting model to feature number 73, Dialister.invisus
2025-06-12 21:40:22.814285 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-06-12 21:40:23.201592 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-06-12 21:40:23.356179 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-06-12 21:40:23.518435 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-06-12 21:40:23.678296 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-06-12 21:40:23.862738 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-06-12 21:40:24.01786 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-06-12 21:40:24.166589 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-06-12 21:40:24.316587 INFO::Fitting model to feature number 82, Escherichia.coli
2025-06-12 21:40:24.48424 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-06-12 21:40:24.631825 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-06-12 21:40:24.768657 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-06-12 21:40:24.91087 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-06-12 21:40:25.062732 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-06-12 21:40:25.262687 INFO::Counting total values for each feature
2025-06-12 21:40:25.295689 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-06-12 21:40:25.424351 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-06-12 21:40:25.572764 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-06-12 21:40:25.710998 INFO::Writing residuals to file output/fits/residuals.rds
2025-06-12 21:40:25.758267 INFO::Writing fitted values to file output/fits/fitted.rds
2025-06-12 21:40:25.784856 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-06-12 21:40:25.792576 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-06-12 21:40:25.802155 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"
2025-06-12 21:40:25.819325 INFO::Writing function arguments to log file
2025-06-12 21:40:25.830165 INFO::Verifying options selected are valid
2025-06-12 21:40:25.831754 INFO::Determining format of input files
2025-06-12 21:40:25.833637 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-12 21:40:25.840971 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-06-12 21:40:25.843003 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-06-12 21:40:25.845669 INFO::Filter data based on min abundance and min prevalence
2025-06-12 21:40:25.847199 INFO::Total samples in data: 1595
2025-06-12 21:40:25.848682 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-06-12 21:40:25.854817 INFO::Total filtered features: 0
2025-06-12 21:40:25.85617 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-12 21:40:25.862653 INFO::Total filtered features with variance filtering: 0
2025-06-12 21:40:25.864056 INFO::Filtered feature names from variance filtering:
2025-06-12 21:40:25.865056 INFO::Running selected normalization method: NONE
2025-06-12 21:40:25.86599 INFO::Bypass z-score application to metadata
2025-06-12 21:40:25.867548 INFO::Running selected transform method: AST
2025-06-12 21:40:25.90074 INFO::Running selected analysis method: LM
2025-06-12 21:40:25.903407 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-06-12 21:40:26.039756 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-06-12 21:40:26.195811 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-06-12 21:40:26.345956 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-06-12 21:40:26.502098 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-06-12 21:40:26.633224 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-06-12 21:40:26.786669 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-06-12 21:40:26.932824 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-06-12 21:40:27.087015 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-06-12 21:40:27.238603 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-06-12 21:40:27.380299 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-06-12 21:40:27.533916 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-06-12 21:40:27.675114 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-06-12 21:40:27.807609 WARNING::Fitting problem for feature 13 a warning was issued
2025-06-12 21:40:27.974675 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-06-12 21:40:28.122675 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-06-12 21:40:28.27788 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-06-12 21:40:28.423674 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-06-12 21:40:28.59097 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-06-12 21:40:28.751035 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-06-12 21:40:28.89677 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-06-12 21:40:29.051432 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-06-12 21:40:29.228475 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-06-12 21:40:29.367547 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-06-12 21:40:29.515555 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-06-12 21:40:29.719248 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-06-12 21:40:29.869069 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-06-12 21:40:30.024835 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-06-12 21:40:30.196589 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-06-12 21:40:30.347662 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-06-12 21:40:30.497779 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-06-12 21:40:30.650154 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-06-12 21:40:30.791729 INFO::Fitting model to feature number 32, Prevotella.copri
2025-06-12 21:40:30.961824 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-06-12 21:40:31.102634 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-06-12 21:40:31.253891 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-06-12 21:40:31.411586 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-06-12 21:40:31.581221 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-06-12 21:40:31.724562 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-06-12 21:40:31.873661 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-06-12 21:40:32.029176 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-06-12 21:40:32.197974 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-06-12 21:40:32.352615 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-06-12 21:40:32.496805 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-06-12 21:40:32.659277 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-06-12 21:40:32.826473 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-06-12 21:40:32.985329 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-06-12 21:40:33.142935 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-06-12 21:40:33.297844 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-06-12 21:40:33.474459 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-06-12 21:40:33.622667 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-06-12 21:40:33.763374 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-06-12 21:40:33.9171 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-06-12 21:40:34.066953 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-06-12 21:40:34.190618 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-06-12 21:40:34.338563 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-06-12 21:40:34.475376 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-06-12 21:40:34.649429 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-06-12 21:40:34.794046 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-06-12 21:40:34.948641 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-06-12 21:40:35.101063 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-06-12 21:40:35.259974 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-06-12 21:40:35.410727 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-06-12 21:40:35.564486 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-06-12 21:40:35.742834 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-06-12 21:40:35.893516 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-06-12 21:40:36.043273 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-06-12 21:40:36.19768 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-06-12 21:40:36.339526 WARNING::Fitting problem for feature 67 a warning was issued
2025-06-12 21:40:36.501323 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-06-12 21:40:36.663378 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-06-12 21:40:36.828948 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-06-12 21:40:36.990342 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-06-12 21:40:37.146787 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-06-12 21:40:37.201741 WARNING::Fitting problem for feature 72 a warning was issued
2025-06-12 21:40:37.340281 INFO::Fitting model to feature number 73, Dialister.invisus
2025-06-12 21:40:37.503246 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-06-12 21:40:37.638194 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-06-12 21:40:37.789944 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-06-12 21:40:37.939795 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-06-12 21:40:38.087965 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-06-12 21:40:38.246276 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-06-12 21:40:38.409121 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-06-12 21:40:38.563928 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-06-12 21:40:38.723988 INFO::Fitting model to feature number 82, Escherichia.coli
2025-06-12 21:40:38.884288 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-06-12 21:40:39.035776 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-06-12 21:40:39.17712 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-06-12 21:40:39.324963 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-06-12 21:40:39.48228 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-06-12 21:40:39.652291 INFO::Counting total values for each feature
2025-06-12 21:40:39.680787 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-06-12 21:40:39.80392 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-06-12 21:40:39.91927 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-06-12 21:40:40.076523 INFO::Writing residuals to file output2/fits/residuals.rds
2025-06-12 21:40:40.145525 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-06-12 21:40:40.209868 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-06-12 21:40:40.216406 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-06-12 21:40:40.224713 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 32.475   0.706  33.341

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin297.115 1.87399.831