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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1148/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz
StartedAt: 2025-08-30 00:05:45 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 00:09:57 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 251.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 86.932  0.824  87.744
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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"
2025-08-30 00:07:42.363805 INFO::Writing function arguments to log file
2025-08-30 00:07:42.401082 INFO::Verifying options selected are valid
2025-08-30 00:07:42.43276 INFO::Determining format of input files
2025-08-30 00:07:42.434186 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-30 00:07:42.438956 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-30 00:07:42.440189 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-30 00:07:42.442486 INFO::Filter data based on min abundance and min prevalence
2025-08-30 00:07:42.443348 INFO::Total samples in data: 1595
2025-08-30 00:07:42.444153 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-30 00:07:42.453659 INFO::Total filtered features: 0
2025-08-30 00:07:42.454782 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-30 00:07:42.460998 INFO::Total filtered features with variance filtering: 0
2025-08-30 00:07:42.461976 INFO::Filtered feature names from variance filtering:
2025-08-30 00:07:42.462811 INFO::Running selected normalization method: TSS
2025-08-30 00:07:43.486636 INFO::Bypass z-score application to metadata
2025-08-30 00:07:43.487918 INFO::Running selected transform method: AST
2025-08-30 00:07:43.504576 INFO::Running selected analysis method: LM
2025-08-30 00:07:44.097311 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-30 00:07:44.542907 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-30 00:07:44.690813 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-30 00:07:44.851805 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-30 00:07:45.003513 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-30 00:07:45.152321 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-30 00:07:45.301198 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-30 00:07:45.457076 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-30 00:07:45.57553 WARNING::Fitting problem for feature 8 a warning was issued
2025-08-30 00:07:45.726188 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-30 00:07:45.845884 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-30 00:07:45.999948 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-30 00:07:46.142177 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-30 00:07:46.326576 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-30 00:07:46.466132 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-30 00:07:46.586205 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-30 00:07:46.738671 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-30 00:07:46.894761 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-30 00:07:47.045803 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-30 00:07:47.197342 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-30 00:07:47.360333 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-30 00:07:47.52292 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-30 00:07:47.676817 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-30 00:07:47.841159 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-30 00:07:47.999864 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-30 00:07:48.149867 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-30 00:07:48.293741 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-30 00:07:48.448084 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-30 00:07:48.593783 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-30 00:07:48.737679 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-30 00:07:48.8926 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-30 00:07:49.038078 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-30 00:07:49.187702 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-30 00:07:49.333955 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-30 00:07:49.483181 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-30 00:07:49.632425 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-30 00:07:49.797466 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-30 00:07:49.949864 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-30 00:07:50.10966 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-30 00:07:50.256845 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-30 00:07:50.403628 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-30 00:07:50.55003 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-30 00:07:50.696584 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-30 00:07:50.852272 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-30 00:07:51.006718 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-30 00:07:51.158149 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-30 00:07:51.311464 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-30 00:07:51.458368 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-30 00:07:51.609018 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-30 00:07:51.77121 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-30 00:07:51.923289 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-30 00:07:52.079351 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-30 00:07:52.227771 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-30 00:07:52.383456 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-30 00:07:52.550043 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-30 00:07:52.731413 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-30 00:07:52.896302 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-30 00:07:53.049114 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-30 00:07:53.196025 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-30 00:07:53.3584 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-30 00:07:53.502595 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-30 00:07:53.668702 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-30 00:07:53.819545 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-30 00:07:53.978337 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-30 00:07:54.130452 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-30 00:07:54.292365 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-30 00:07:54.468241 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-30 00:07:54.609108 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-30 00:07:54.751567 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-30 00:07:54.906283 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-30 00:07:55.05066 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-30 00:07:55.209005 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-30 00:07:55.376064 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-30 00:07:55.54129 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-30 00:07:55.694665 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-30 00:07:55.840302 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-30 00:07:55.997689 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-30 00:07:56.154964 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-30 00:07:56.316526 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-30 00:07:56.483731 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-30 00:07:56.640938 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-30 00:07:56.80045 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-30 00:07:56.961286 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-30 00:07:57.114554 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-30 00:07:57.284203 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-30 00:07:57.439847 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-30 00:07:57.590994 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-30 00:07:57.750968 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-30 00:07:57.901141 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-30 00:07:58.0541 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-30 00:07:58.251447 INFO::Counting total values for each feature
2025-08-30 00:07:58.283237 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-30 00:07:58.378147 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-30 00:07:58.474286 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-30 00:07:58.572644 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-30 00:07:58.621133 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-30 00:07:58.946697 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-30 00:07:58.953087 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-30 00:07:58.958412 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"
2025-08-30 00:07:58.970468 INFO::Writing function arguments to log file
2025-08-30 00:07:58.976033 INFO::Verifying options selected are valid
2025-08-30 00:07:58.977021 INFO::Determining format of input files
2025-08-30 00:07:58.978204 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-30 00:07:58.983213 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-30 00:07:58.984288 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-30 00:07:58.985878 INFO::Filter data based on min abundance and min prevalence
2025-08-30 00:07:58.986739 INFO::Total samples in data: 1595
2025-08-30 00:07:58.98757 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-30 00:07:58.991479 INFO::Total filtered features: 0
2025-08-30 00:07:58.992435 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-30 00:07:58.9987 INFO::Total filtered features with variance filtering: 0
2025-08-30 00:07:58.999757 INFO::Filtered feature names from variance filtering:
2025-08-30 00:07:59.000608 INFO::Running selected normalization method: NONE
2025-08-30 00:07:59.001429 INFO::Bypass z-score application to metadata
2025-08-30 00:07:59.00224 INFO::Running selected transform method: AST
2025-08-30 00:07:59.015615 INFO::Running selected analysis method: LM
2025-08-30 00:07:59.017402 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-30 00:07:59.158382 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-30 00:07:59.309296 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-30 00:07:59.444399 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-30 00:07:59.580552 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-30 00:07:59.720724 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-30 00:07:59.866399 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-30 00:08:00.00133 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-30 00:08:00.133957 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-30 00:08:00.277908 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-30 00:08:00.421969 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-30 00:08:00.569195 WARNING::Fitting problem for feature 11 a warning was issued
2025-08-30 00:08:00.73132 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-30 00:08:00.887607 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-30 00:08:01.029345 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-30 00:08:01.164926 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-30 00:08:01.310454 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-30 00:08:01.421352 WARNING::Fitting problem for feature 16 a warning was issued
2025-08-30 00:08:01.563631 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-30 00:08:01.717724 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-30 00:08:01.86081 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-30 00:08:01.996233 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-30 00:08:02.144754 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-30 00:08:02.288737 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-30 00:08:02.437212 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-30 00:08:02.594156 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-30 00:08:02.748759 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-30 00:08:02.891608 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-30 00:08:03.036529 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-30 00:08:03.182708 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-30 00:08:03.327894 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-30 00:08:03.458161 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-30 00:08:03.592233 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-30 00:08:03.971667 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-30 00:08:04.113258 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-30 00:08:04.261657 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-30 00:08:04.413271 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-30 00:08:04.564874 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-30 00:08:04.701402 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-30 00:08:04.841227 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-30 00:08:04.978262 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-30 00:08:05.11182 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-30 00:08:05.242147 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-30 00:08:05.378511 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-30 00:08:05.522616 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-30 00:08:05.66126 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-30 00:08:05.798156 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-30 00:08:05.933007 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-30 00:08:06.080571 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-30 00:08:06.21229 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-30 00:08:06.354776 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-30 00:08:06.49131 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-30 00:08:06.625435 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-30 00:08:06.760051 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-30 00:08:06.88468 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-30 00:08:07.015604 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-30 00:08:07.147003 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-30 00:08:07.283222 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-30 00:08:07.418555 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-30 00:08:07.555456 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-30 00:08:07.686582 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-30 00:08:07.822904 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-30 00:08:07.960368 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-30 00:08:08.094203 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-30 00:08:08.231281 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-30 00:08:08.375052 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-30 00:08:08.510811 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-30 00:08:08.647096 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-30 00:08:08.786739 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-30 00:08:08.899812 WARNING::Fitting problem for feature 67 a warning was issued
2025-08-30 00:08:09.046601 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-30 00:08:09.181652 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-30 00:08:09.318666 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-30 00:08:09.45971 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-30 00:08:09.811019 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-30 00:08:09.858524 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-30 00:08:09.993971 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-30 00:08:10.13404 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-30 00:08:10.276095 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-30 00:08:10.419013 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-30 00:08:10.557109 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-30 00:08:10.693936 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-30 00:08:10.833812 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-30 00:08:10.982936 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-30 00:08:11.114848 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-30 00:08:11.255703 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-30 00:08:11.390734 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-30 00:08:11.530563 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-30 00:08:11.663329 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-30 00:08:11.797328 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-30 00:08:11.93545 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-30 00:08:12.100838 INFO::Counting total values for each feature
2025-08-30 00:08:12.122346 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-30 00:08:12.215058 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-30 00:08:12.30798 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-30 00:08:12.404741 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-30 00:08:12.468496 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-30 00:08:12.530035 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-30 00:08:12.535311 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-30 00:08:12.539509 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.731   0.519  31.242

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin286.932 0.82487.744