Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-22 11:43 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4547
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 1141/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 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
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
kunpeng2Linux (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: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2025-03-21 22:02:07 -0400 (Fri, 21 Mar 2025)
EndedAt: 2025-03-21 22:05:08 -0400 (Fri, 21 Mar 2025)
EllapsedTime: 181.6 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* 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 ‘1.21.0’
* 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 97.102  1.835  99.733
* 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-3.21-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 ‘1.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.16
Current TMB package version is 1.9.17
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
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"
2025-03-21 22:04:26.034825 INFO::Writing function arguments to log file
2025-03-21 22:04:26.08869 INFO::Verifying options selected are valid
2025-03-21 22:04:26.131504 INFO::Determining format of input files
2025-03-21 22:04:26.133709 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 22:04:26.1423 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 22:04:26.1445 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-21 22:04:26.14839 INFO::Filter data based on min abundance and min prevalence
2025-03-21 22:04:26.149979 INFO::Total samples in data: 1595
2025-03-21 22:04:26.151514 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 22:04:26.167687 INFO::Total filtered features: 0
2025-03-21 22:04:26.169243 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 22:04:26.180296 INFO::Total filtered features with variance filtering: 0
2025-03-21 22:04:26.182269 INFO::Filtered feature names from variance filtering:
2025-03-21 22:04:26.183942 INFO::Running selected normalization method: TSS
2025-03-21 22:04:27.49545 INFO::Bypass z-score application to metadata
2025-03-21 22:04:27.497492 INFO::Running selected transform method: AST
2025-03-21 22:04:27.518267 INFO::Running selected analysis method: LM
2025-03-21 22:04:28.151995 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 22:04:28.5488 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 22:04:28.742504 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 22:04:28.951159 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 22:04:29.14515 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 22:04:29.338674 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 22:04:29.522119 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 22:04:29.698597 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 22:04:29.891849 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 22:04:30.067071 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 22:04:30.258142 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 22:04:30.420008 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 22:04:30.57197 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 22:04:30.71834 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-21 22:04:30.897111 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 22:04:31.064323 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 22:04:31.286099 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 22:04:31.442231 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 22:04:31.608046 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 22:04:31.784043 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 22:04:31.952902 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 22:04:32.117812 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 22:04:32.289712 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 22:04:32.465834 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 22:04:32.624956 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 22:04:32.793854 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 22:04:32.95169 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 22:04:33.106499 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 22:04:33.281219 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 22:04:33.466943 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 22:04:33.636731 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 22:04:33.802881 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 22:04:33.995897 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 22:04:34.156209 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 22:04:34.337814 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 22:04:34.519467 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 22:04:34.691127 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 22:04:34.862309 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 22:04:35.047297 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 22:04:35.202233 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 22:04:35.377099 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 22:04:35.544442 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 22:04:35.714898 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 22:04:35.896794 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 22:04:36.073827 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 22:04:36.237134 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 22:04:36.396385 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 22:04:36.558621 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 22:04:36.740069 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 22:04:36.907903 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 22:04:37.09528 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 22:04:37.25295 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 22:04:37.673512 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 22:04:37.81894 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 22:04:37.988702 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 22:04:38.157111 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 22:04:38.314756 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 22:04:38.460139 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 22:04:38.596904 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 22:04:38.755136 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 22:04:38.917059 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 22:04:39.073847 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 22:04:39.215525 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 22:04:39.370944 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 22:04:39.543931 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 22:04:39.69398 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 22:04:39.836713 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 22:04:39.994959 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 22:04:40.139777 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 22:04:40.299189 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 22:04:40.465474 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 22:04:40.634554 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 22:04:40.806859 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 22:04:40.960152 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 22:04:41.122936 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 22:04:41.291984 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 22:04:41.455482 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 22:04:41.628475 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 22:04:41.794072 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 22:04:41.972946 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 22:04:42.143056 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 22:04:42.295622 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 22:04:42.460829 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 22:04:42.636365 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 22:04:42.791878 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 22:04:42.951797 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 22:04:43.112239 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 22:04:43.271424 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 22:04:43.490547 INFO::Counting total values for each feature
2025-03-21 22:04:43.52368 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-21 22:04:43.651076 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-21 22:04:43.804089 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-21 22:04:43.982173 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-21 22:04:44.04328 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-21 22:04:44.075506 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-21 22:04:44.083585 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-21 22:04:44.09608 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"
2025-03-21 22:04:44.116387 INFO::Writing function arguments to log file
2025-03-21 22:04:44.12766 INFO::Verifying options selected are valid
2025-03-21 22:04:44.129355 INFO::Determining format of input files
2025-03-21 22:04:44.131316 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 22:04:44.138983 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 22:04:44.140884 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-21 22:04:44.143445 INFO::Filter data based on min abundance and min prevalence
2025-03-21 22:04:44.144966 INFO::Total samples in data: 1595
2025-03-21 22:04:44.146475 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 22:04:44.150809 INFO::Total filtered features: 0
2025-03-21 22:04:44.152324 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 22:04:44.170689 INFO::Total filtered features with variance filtering: 0
2025-03-21 22:04:44.172304 INFO::Filtered feature names from variance filtering:
2025-03-21 22:04:44.173546 INFO::Running selected normalization method: NONE
2025-03-21 22:04:44.174728 INFO::Bypass z-score application to metadata
2025-03-21 22:04:44.175671 INFO::Running selected transform method: AST
2025-03-21 22:04:44.190127 INFO::Running selected analysis method: LM
2025-03-21 22:04:44.191855 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 22:04:44.339405 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 22:04:44.502099 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 22:04:44.649024 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 22:04:44.827558 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 22:04:44.979045 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 22:04:45.130846 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 22:04:45.291019 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 22:04:45.453381 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 22:04:45.8337 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 22:04:45.99118 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 22:04:46.134775 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 22:04:46.280669 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 22:04:46.419579 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-21 22:04:46.599556 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 22:04:46.743939 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 22:04:46.87958 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 22:04:47.02529 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 22:04:47.179159 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 22:04:47.323592 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 22:04:47.459886 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 22:04:47.617561 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 22:04:47.758199 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 22:04:47.908477 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 22:04:48.063003 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 22:04:48.212003 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 22:04:48.356193 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 22:04:48.522449 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 22:04:48.676724 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 22:04:48.823047 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 22:04:48.984581 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 22:04:49.12418 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 22:04:49.279733 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 22:04:49.436997 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 22:04:49.583322 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 22:04:49.737326 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 22:04:49.90002 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 22:04:50.057977 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 22:04:50.215459 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 22:04:50.371798 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 22:04:50.513821 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 22:04:50.658531 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 22:04:50.814045 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 22:04:50.962331 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 22:04:51.34231 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 22:04:51.495175 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 22:04:51.647142 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 22:04:51.789529 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 22:04:51.946322 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 22:04:52.098451 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 22:04:52.258267 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 22:04:52.397938 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 22:04:52.781548 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 22:04:52.911818 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 22:04:53.045166 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 22:04:53.195231 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 22:04:53.36711 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 22:04:53.527392 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 22:04:53.6661 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 22:04:53.825942 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 22:04:54.000084 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 22:04:54.14407 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 22:04:54.298511 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 22:04:54.451517 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 22:04:54.631303 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 22:04:54.798869 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 22:04:54.961306 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 22:04:55.127749 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 22:04:55.272325 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-21 22:04:55.42694 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 22:04:55.585423 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 22:04:55.754721 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 22:04:55.937695 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 22:04:56.079166 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 22:04:56.134589 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-21 22:04:56.302921 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 22:04:56.478633 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 22:04:56.644695 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 22:04:56.812421 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 22:04:56.983369 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 22:04:57.148142 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 22:04:57.312027 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 22:04:57.478274 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 22:04:57.628408 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 22:04:57.785466 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 22:04:57.929741 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 22:04:58.068834 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 22:04:58.214901 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 22:04:58.365227 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 22:04:58.523696 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 22:04:58.71376 INFO::Counting total values for each feature
2025-03-21 22:04:58.739367 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-21 22:04:58.868426 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-21 22:04:58.988382 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-21 22:04:59.140173 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-21 22:04:59.456383 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-21 22:04:59.527088 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-21 22:04:59.533903 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-21 22:04:59.541264 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 
 34.076   0.758  35.034

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin297.102 1.83599.733