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This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1146/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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
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 13.7.7 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 palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Maaslin2_1.23.0.tar.gz
StartedAt: 2025-08-15 04:41:53 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 04:45:15 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 201.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Maaslin2_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 107.2   7.41  114.92
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2025-08-15 04:44:29.427572 INFO::Writing function arguments to log file
2025-08-15 04:44:29.471795 INFO::Verifying options selected are valid
2025-08-15 04:44:29.511811 INFO::Determining format of input files
2025-08-15 04:44:29.514617 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 04:44:29.535762 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-15 04:44:29.539271 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-15 04:44:29.543217 INFO::Filter data based on min abundance and min prevalence
2025-08-15 04:44:29.544906 INFO::Total samples in data: 1595
2025-08-15 04:44:29.546596 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-15 04:44:29.552197 INFO::Total filtered features: 0
2025-08-15 04:44:29.55413 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-15 04:44:29.565105 INFO::Total filtered features with variance filtering: 0
2025-08-15 04:44:29.567144 INFO::Filtered feature names from variance filtering:
2025-08-15 04:44:29.568855 INFO::Running selected normalization method: TSS
2025-08-15 04:44:30.895313 INFO::Bypass z-score application to metadata
2025-08-15 04:44:30.898591 INFO::Running selected transform method: AST
2025-08-15 04:44:30.927112 INFO::Running selected analysis method: LM
2025-08-15 04:44:31.774924 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-15 04:44:32.348045 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-15 04:44:32.534593 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-15 04:44:32.782041 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-15 04:44:32.999858 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-15 04:44:33.224334 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-15 04:44:33.445179 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-15 04:44:33.672415 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-15 04:44:33.844189 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-15 04:44:34.00176 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-15 04:44:34.191179 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-15 04:44:34.361526 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-15 04:44:34.569791 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-15 04:44:34.737536 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-15 04:44:34.890214 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-15 04:44:35.032631 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-15 04:44:35.176035 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-15 04:44:35.37889 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-15 04:44:35.595739 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-15 04:44:35.817127 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-15 04:44:36.045052 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-15 04:44:36.260476 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-15 04:44:36.409067 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-15 04:44:36.556466 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-15 04:44:36.72851 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-15 04:44:36.929185 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-15 04:44:37.153521 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-15 04:44:37.363409 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-15 04:44:37.578723 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-15 04:44:37.751327 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-15 04:44:37.914868 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-15 04:44:38.128387 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-15 04:44:38.355576 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-15 04:44:38.541552 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-15 04:44:38.71588 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-15 04:44:38.877932 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-15 04:44:39.060299 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-15 04:44:39.231237 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-15 04:44:39.416745 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-15 04:44:39.588322 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-15 04:44:39.795791 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-15 04:44:39.991891 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-15 04:44:40.182732 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-15 04:44:40.343566 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-15 04:44:40.507188 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-15 04:44:40.652684 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-15 04:44:40.853579 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-15 04:44:41.09023 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-15 04:44:41.321579 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-15 04:44:41.54367 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-15 04:44:41.698601 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-15 04:44:41.835903 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-15 04:44:41.980621 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-15 04:44:42.149232 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-15 04:44:42.37677 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-15 04:44:42.599503 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-15 04:44:42.752382 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-15 04:44:42.93486 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-15 04:44:43.118528 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-15 04:44:43.301941 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-15 04:44:43.433092 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-15 04:44:43.567879 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-15 04:44:43.701763 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-15 04:44:43.84077 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-15 04:44:44.008297 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-15 04:44:44.16135 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-15 04:44:44.343097 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-15 04:44:44.568076 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-15 04:44:44.774168 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-15 04:44:44.965324 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-15 04:44:45.153799 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-15 04:44:45.33064 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-15 04:44:45.487123 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-15 04:44:45.646558 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-15 04:44:45.840528 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-15 04:44:46.050603 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-15 04:44:46.263762 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-15 04:44:46.473755 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-15 04:44:46.69285 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-15 04:44:46.942753 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-15 04:44:47.127069 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-15 04:44:47.255694 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-15 04:44:47.444424 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-15 04:44:47.652457 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-15 04:44:47.863679 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-15 04:44:48.041527 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-15 04:44:48.173388 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-15 04:44:48.314209 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-15 04:44:48.485629 INFO::Counting total values for each feature
2025-08-15 04:44:48.543504 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-15 04:44:49.035807 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-15 04:44:49.570972 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-15 04:44:49.957316 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-15 04:44:50.017654 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-15 04:44:50.05307 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-15 04:44:50.062224 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-15 04:44:50.087961 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"
2025-08-15 04:44:50.151771 INFO::Writing function arguments to log file
2025-08-15 04:44:50.16617 INFO::Verifying options selected are valid
2025-08-15 04:44:50.167996 INFO::Determining format of input files
2025-08-15 04:44:50.170104 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-15 04:44:50.177765 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-15 04:44:50.17968 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-15 04:44:50.182163 INFO::Filter data based on min abundance and min prevalence
2025-08-15 04:44:50.183858 INFO::Total samples in data: 1595
2025-08-15 04:44:50.185495 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-15 04:44:50.19149 INFO::Total filtered features: 0
2025-08-15 04:44:50.193417 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-15 04:44:50.202946 INFO::Total filtered features with variance filtering: 0
2025-08-15 04:44:50.205067 INFO::Filtered feature names from variance filtering:
2025-08-15 04:44:50.206883 INFO::Running selected normalization method: NONE
2025-08-15 04:44:50.208556 INFO::Bypass z-score application to metadata
2025-08-15 04:44:50.210229 INFO::Running selected transform method: AST
2025-08-15 04:44:50.232151 INFO::Running selected analysis method: LM
2025-08-15 04:44:50.235191 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-15 04:44:50.382844 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-15 04:44:50.541418 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-15 04:44:50.972973 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-15 04:44:51.098113 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-15 04:44:51.257343 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-15 04:44:51.39243 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-15 04:44:51.544493 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-15 04:44:51.689292 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-15 04:44:51.850492 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-15 04:44:52.027258 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-15 04:44:52.161581 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-15 04:44:52.315403 WARNING::Fitting problem for feature 11 a warning was issued
2025-08-15 04:44:52.521231 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-15 04:44:52.68787 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-15 04:44:52.853364 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-15 04:44:52.974391 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-15 04:44:53.146711 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-15 04:44:53.321096 WARNING::Fitting problem for feature 16 a warning was issued
2025-08-15 04:44:53.484356 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-15 04:44:53.609121 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-15 04:44:53.735088 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-15 04:44:53.865685 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-15 04:44:53.987767 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-15 04:44:54.173568 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-15 04:44:54.358286 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-15 04:44:54.477251 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-15 04:44:54.663072 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-15 04:44:54.853902 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-15 04:44:54.985277 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-15 04:44:55.134622 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-15 04:44:55.252684 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-15 04:44:55.378061 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-15 04:44:55.493762 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-15 04:44:55.611956 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-15 04:44:55.749869 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-15 04:44:55.869396 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-15 04:44:56.060157 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-15 04:44:56.28317 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-15 04:44:56.412613 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-15 04:44:56.580136 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-15 04:44:56.733048 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-15 04:44:56.885686 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-15 04:44:57.02149 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-15 04:44:57.153564 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-15 04:44:57.321508 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-15 04:44:57.456288 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-15 04:44:57.590648 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-15 04:44:57.781527 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-15 04:44:57.98842 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-15 04:44:58.15485 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-15 04:44:58.35654 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-15 04:44:58.572864 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-15 04:44:58.762756 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-15 04:44:58.966434 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-15 04:44:59.156197 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-15 04:44:59.344237 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-15 04:44:59.500316 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-15 04:44:59.641701 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-15 04:44:59.79372 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-15 04:44:59.919166 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-15 04:45:00.071264 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-15 04:45:00.204638 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-15 04:45:00.34645 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-15 04:45:00.545021 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-15 04:45:00.75422 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-15 04:45:00.924006 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-15 04:45:01.070109 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-15 04:45:01.255453 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-15 04:45:01.425029 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-15 04:45:01.565376 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-15 04:45:01.705157 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-15 04:45:01.839873 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-15 04:45:01.982129 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-15 04:45:02.126461 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-15 04:45:02.1783 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-15 04:45:02.310554 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-15 04:45:02.445686 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-15 04:45:02.579016 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-15 04:45:02.712025 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-15 04:45:02.846946 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-15 04:45:03.003672 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-15 04:45:03.218107 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-15 04:45:03.429059 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-15 04:45:03.573582 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-15 04:45:03.697959 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-15 04:45:03.880789 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-15 04:45:04.05021 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-15 04:45:04.230189 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-15 04:45:04.431991 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-15 04:45:04.63151 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-15 04:45:04.816282 INFO::Counting total values for each feature
2025-08-15 04:45:04.852722 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-15 04:45:05.267717 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-15 04:45:05.673316 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-15 04:45:06.028686 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-15 04:45:06.103178 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-15 04:45:06.468849 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-15 04:45:06.478132 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-15 04:45:06.493946 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  37.46    1.01   38.57

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2107.20 7.41114.92