Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-08-11 11:40 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-07 13:40 -0400 (Thu, 07 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on nebbiolo1

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: 1.22.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.22.0.tar.gz
StartedAt: 2025-08-10 23:46:35 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 23:50:42 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 247.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.2 LTS
* using session charset: UTF-8
* 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 86.412  0.904  87.308
* 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-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 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"
2025-08-10 23:48:31.337206 INFO::Writing function arguments to log file
2025-08-10 23:48:31.374316 INFO::Verifying options selected are valid
2025-08-10 23:48:31.406463 INFO::Determining format of input files
2025-08-10 23:48:31.407933 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 23:48:31.412758 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-10 23:48:31.414024 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-10 23:48:31.416328 INFO::Filter data based on min abundance and min prevalence
2025-08-10 23:48:31.417228 INFO::Total samples in data: 1595
2025-08-10 23:48:31.418054 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-10 23:48:31.42741 INFO::Total filtered features: 0
2025-08-10 23:48:31.428587 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-10 23:48:31.434844 INFO::Total filtered features with variance filtering: 0
2025-08-10 23:48:31.435862 INFO::Filtered feature names from variance filtering:
2025-08-10 23:48:31.436736 INFO::Running selected normalization method: TSS
2025-08-10 23:48:32.442961 INFO::Bypass z-score application to metadata
2025-08-10 23:48:32.444383 INFO::Running selected transform method: AST
2025-08-10 23:48:32.461301 INFO::Running selected analysis method: LM
2025-08-10 23:48:33.068897 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-10 23:48:33.526668 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-10 23:48:33.674185 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-10 23:48:33.831144 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-10 23:48:33.977165 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-10 23:48:34.123038 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-10 23:48:34.267077 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-10 23:48:34.425475 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-10 23:48:34.541832 WARNING::Fitting problem for feature 8 a warning was issued
2025-08-10 23:48:34.692862 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-10 23:48:34.810469 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-10 23:48:34.962511 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-10 23:48:35.100449 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-10 23:48:35.270387 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-10 23:48:35.406772 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-10 23:48:35.524265 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-10 23:48:35.673966 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-10 23:48:35.823895 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-10 23:48:35.969711 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-10 23:48:36.110848 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-10 23:48:36.262026 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-10 23:48:36.405333 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-10 23:48:36.550124 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-10 23:48:36.714387 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-10 23:48:36.86455 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-10 23:48:37.010996 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-10 23:48:37.149452 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-10 23:48:37.299285 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-10 23:48:37.448108 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-10 23:48:37.588448 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-10 23:48:37.742501 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-10 23:48:37.887681 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-10 23:48:38.032991 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-10 23:48:38.176108 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-10 23:48:38.320602 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-10 23:48:38.464952 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-10 23:48:38.617564 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-10 23:48:38.75877 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-10 23:48:38.918237 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-10 23:48:39.065903 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-10 23:48:39.213873 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-10 23:48:39.3559 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-10 23:48:39.495512 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-10 23:48:39.643889 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-10 23:48:39.795203 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-10 23:48:39.944968 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-10 23:48:40.092977 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-10 23:48:40.232287 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-10 23:48:40.377059 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-10 23:48:40.531315 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-10 23:48:40.679415 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-10 23:48:40.832213 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-10 23:48:40.976449 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-10 23:48:41.126709 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-10 23:48:41.268019 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-10 23:48:41.431048 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-10 23:48:41.607733 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-10 23:48:41.776851 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-10 23:48:41.932606 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-10 23:48:42.096566 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-10 23:48:42.236102 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-10 23:48:42.400649 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-10 23:48:42.545573 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-10 23:48:42.691071 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-10 23:48:42.836796 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-10 23:48:42.986712 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-10 23:48:43.165262 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-10 23:48:43.310219 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-10 23:48:43.457564 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-10 23:48:43.620066 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-10 23:48:43.756366 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-10 23:48:43.898769 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-10 23:48:44.046428 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-10 23:48:44.208333 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-10 23:48:44.358068 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-10 23:48:44.515304 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-10 23:48:44.688733 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-10 23:48:44.832966 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-10 23:48:44.975749 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-10 23:48:45.129048 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-10 23:48:45.274522 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-10 23:48:45.425924 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-10 23:48:45.580577 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-10 23:48:45.720829 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-10 23:48:45.873269 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-10 23:48:46.018854 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-10 23:48:46.15984 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-10 23:48:46.311835 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-10 23:48:46.459737 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-10 23:48:46.613737 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-10 23:48:46.817948 INFO::Counting total values for each feature
2025-08-10 23:48:46.848755 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-10 23:48:46.942371 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-10 23:48:47.037365 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-10 23:48:47.134748 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-10 23:48:47.184009 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-10 23:48:47.465669 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-10 23:48:47.472353 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-10 23:48:47.47775 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"
2025-08-10 23:48:47.490323 INFO::Writing function arguments to log file
2025-08-10 23:48:47.496541 INFO::Verifying options selected are valid
2025-08-10 23:48:47.497667 INFO::Determining format of input files
2025-08-10 23:48:47.498929 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-10 23:48:47.504001 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-10 23:48:47.50508 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-10 23:48:47.506723 INFO::Filter data based on min abundance and min prevalence
2025-08-10 23:48:47.50759 INFO::Total samples in data: 1595
2025-08-10 23:48:47.508467 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-10 23:48:47.512371 INFO::Total filtered features: 0
2025-08-10 23:48:47.513338 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-10 23:48:47.519548 INFO::Total filtered features with variance filtering: 0
2025-08-10 23:48:47.520567 INFO::Filtered feature names from variance filtering:
2025-08-10 23:48:47.521413 INFO::Running selected normalization method: NONE
2025-08-10 23:48:47.522273 INFO::Bypass z-score application to metadata
2025-08-10 23:48:47.523107 INFO::Running selected transform method: AST
2025-08-10 23:48:47.537571 INFO::Running selected analysis method: LM
2025-08-10 23:48:47.539303 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-10 23:48:47.677733 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-10 23:48:47.831431 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-10 23:48:47.973204 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-10 23:48:48.115022 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-10 23:48:48.247178 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-10 23:48:48.39108 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-10 23:48:48.522926 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-10 23:48:48.65737 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-10 23:48:48.802332 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-10 23:48:48.939024 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-10 23:48:49.055491 WARNING::Fitting problem for feature 11 a warning was issued
2025-08-10 23:48:49.201649 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-10 23:48:49.348462 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-10 23:48:49.497607 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-10 23:48:49.644214 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-10 23:48:49.804575 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-10 23:48:49.915931 WARNING::Fitting problem for feature 16 a warning was issued
2025-08-10 23:48:50.055343 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-10 23:48:50.204303 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-10 23:48:50.339709 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-10 23:48:50.473458 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-10 23:48:50.622616 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-10 23:48:50.76145 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-10 23:48:50.898449 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-10 23:48:51.031605 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-10 23:48:51.168332 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-10 23:48:51.30414 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-10 23:48:51.439216 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-10 23:48:51.575715 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-10 23:48:51.709042 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-10 23:48:51.835569 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-10 23:48:51.96594 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-10 23:48:52.353903 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-10 23:48:52.489154 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-10 23:48:52.623755 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-10 23:48:52.760229 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-10 23:48:52.899292 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-10 23:48:53.0386 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-10 23:48:53.182323 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-10 23:48:53.323506 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-10 23:48:53.463883 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-10 23:48:53.593922 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-10 23:48:53.725131 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-10 23:48:53.864543 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-10 23:48:53.998885 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-10 23:48:54.133447 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-10 23:48:54.266677 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-10 23:48:54.410319 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-10 23:48:54.53849 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-10 23:48:54.672589 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-10 23:48:54.824421 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-10 23:48:54.959177 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-10 23:48:55.094914 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-10 23:48:55.222588 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-10 23:48:55.351434 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-10 23:48:55.479816 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-10 23:48:55.609783 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-10 23:48:55.74269 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-10 23:48:55.877602 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-10 23:48:56.006507 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-10 23:48:56.141007 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-10 23:48:56.272965 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-10 23:48:56.402066 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-10 23:48:56.532412 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-10 23:48:56.674603 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-10 23:48:56.807247 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-10 23:48:56.938832 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-10 23:48:57.079286 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-10 23:48:57.193952 WARNING::Fitting problem for feature 67 a warning was issued
2025-08-10 23:48:57.336956 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-10 23:48:57.47562 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-10 23:48:57.614222 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-10 23:48:57.756019 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-10 23:48:57.89498 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-10 23:48:57.941556 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-10 23:48:58.072816 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-10 23:48:58.211978 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-10 23:48:58.344904 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-10 23:48:58.484607 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-10 23:48:58.634362 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-10 23:48:58.766846 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-10 23:48:58.913663 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-10 23:48:59.053819 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-10 23:48:59.190078 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-10 23:48:59.339537 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-10 23:48:59.473265 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-10 23:48:59.616075 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-10 23:48:59.752597 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-10 23:48:59.89015 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-10 23:49:00.028114 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-10 23:49:00.194861 INFO::Counting total values for each feature
2025-08-10 23:49:00.216419 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-10 23:49:00.309262 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-10 23:49:00.401908 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-10 23:49:00.49907 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-10 23:49:00.817265 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-10 23:49:00.880688 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-10 23:49:00.886196 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-10 23:49:00.890582 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 
 30.118   0.497  30.607

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin286.412 0.90487.308