Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-21 11:44 -0400 (Fri, 21 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" 4545
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: 2025-03-20 13:40 -0400 (Thu, 20 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: 2025-03-20 21:54:08 -0400 (Thu, 20 Mar 2025)
EndedAt: 2025-03-20 21:57:08 -0400 (Thu, 20 Mar 2025)
EllapsedTime: 179.5 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 97.104  1.887  99.819
* 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"
2025-03-20 21:56:27.425524 INFO::Writing function arguments to log file
2025-03-20 21:56:27.482485 INFO::Verifying options selected are valid
2025-03-20 21:56:27.526283 INFO::Determining format of input files
2025-03-20 21:56:27.528436 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-20 21:56:27.536346 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-20 21:56:27.538367 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-20 21:56:27.542281 INFO::Filter data based on min abundance and min prevalence
2025-03-20 21:56:27.54356 INFO::Total samples in data: 1595
2025-03-20 21:56:27.545277 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-20 21:56:27.558974 INFO::Total filtered features: 0
2025-03-20 21:56:27.561038 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-20 21:56:27.57098 INFO::Total filtered features with variance filtering: 0
2025-03-20 21:56:27.572771 INFO::Filtered feature names from variance filtering:
2025-03-20 21:56:27.574249 INFO::Running selected normalization method: TSS
2025-03-20 21:56:28.881346 INFO::Bypass z-score application to metadata
2025-03-20 21:56:28.882997 INFO::Running selected transform method: AST
2025-03-20 21:56:28.900866 INFO::Running selected analysis method: LM
2025-03-20 21:56:29.511651 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-20 21:56:29.945008 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-20 21:56:30.120125 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-20 21:56:30.31069 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-20 21:56:30.494485 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-20 21:56:30.677587 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-20 21:56:30.852156 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-20 21:56:31.032994 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-20 21:56:31.180129 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-20 21:56:31.335947 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-20 21:56:31.507576 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-20 21:56:31.68161 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-20 21:56:31.846329 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-20 21:56:31.98983 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-20 21:56:32.166033 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-20 21:56:32.342901 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-20 21:56:32.539763 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-20 21:56:32.703327 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-20 21:56:32.871308 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-20 21:56:33.038225 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-20 21:56:33.195186 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-20 21:56:33.35133 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-20 21:56:33.516641 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-20 21:56:33.684094 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-20 21:56:33.842401 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-20 21:56:33.989033 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-20 21:56:34.163402 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-20 21:56:34.316944 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-20 21:56:34.499468 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-20 21:56:34.68779 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-20 21:56:34.873022 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-20 21:56:35.039885 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-20 21:56:35.221893 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-20 21:56:35.407771 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-20 21:56:35.592449 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-20 21:56:35.762655 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-20 21:56:35.927712 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-20 21:56:36.091831 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-20 21:56:36.265491 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-20 21:56:36.424311 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-20 21:56:36.594542 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-20 21:56:36.761766 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-20 21:56:36.93318 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-20 21:56:37.110861 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-20 21:56:37.26126 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-20 21:56:37.430186 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-20 21:56:37.584787 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-20 21:56:37.738932 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-20 21:56:37.918934 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-20 21:56:38.068596 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-20 21:56:38.236466 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-20 21:56:38.384919 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-20 21:56:38.551659 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-20 21:56:38.704144 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-20 21:56:38.88577 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-20 21:56:39.041111 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-20 21:56:39.211627 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-20 21:56:39.373699 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-20 21:56:39.535349 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-20 21:56:39.702982 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-20 21:56:39.872502 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-20 21:56:40.032876 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-20 21:56:40.188402 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-20 21:56:40.373311 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-20 21:56:40.532552 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-20 21:56:40.706833 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-20 21:56:40.873192 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-20 21:56:41.043606 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-20 21:56:41.21437 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-20 21:56:41.369743 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-20 21:56:41.525537 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-20 21:56:41.679651 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-20 21:56:42.054075 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-20 21:56:42.188462 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-20 21:56:42.324994 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-20 21:56:42.489593 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-20 21:56:42.65813 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-20 21:56:42.815213 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-20 21:56:42.96201 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-20 21:56:43.125238 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-20 21:56:43.289129 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-20 21:56:43.437046 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-20 21:56:43.592527 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-20 21:56:43.743523 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-20 21:56:43.872569 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-20 21:56:44.013521 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-20 21:56:44.14111 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-20 21:56:44.297367 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-20 21:56:44.479189 INFO::Counting total values for each feature
2025-03-20 21:56:44.514885 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-20 21:56:44.630875 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-20 21:56:44.787304 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-20 21:56:44.932762 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-20 21:56:44.983978 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-20 21:56:45.012199 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-20 21:56:45.018822 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-20 21:56:45.026936 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"
2025-03-20 21:56:45.045382 INFO::Writing function arguments to log file
2025-03-20 21:56:45.054081 INFO::Verifying options selected are valid
2025-03-20 21:56:45.055288 INFO::Determining format of input files
2025-03-20 21:56:45.056559 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-20 21:56:45.062818 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-20 21:56:45.064321 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-20 21:56:45.066428 INFO::Filter data based on min abundance and min prevalence
2025-03-20 21:56:45.067421 INFO::Total samples in data: 1595
2025-03-20 21:56:45.068721 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-20 21:56:45.07271 INFO::Total filtered features: 0
2025-03-20 21:56:45.074542 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-20 21:56:45.082035 INFO::Total filtered features with variance filtering: 0
2025-03-20 21:56:45.083741 INFO::Filtered feature names from variance filtering:
2025-03-20 21:56:45.084909 INFO::Running selected normalization method: NONE
2025-03-20 21:56:45.086201 INFO::Bypass z-score application to metadata
2025-03-20 21:56:45.08717 INFO::Running selected transform method: AST
2025-03-20 21:56:45.111963 INFO::Running selected analysis method: LM
2025-03-20 21:56:45.11383 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-20 21:56:45.250614 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-20 21:56:45.394883 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-20 21:56:45.540473 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-20 21:56:45.698503 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-20 21:56:45.832647 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-20 21:56:45.992947 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-20 21:56:46.384991 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-20 21:56:46.540608 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-20 21:56:46.692087 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-20 21:56:46.84799 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-20 21:56:47.003068 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-20 21:56:47.153983 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-20 21:56:47.282049 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-20 21:56:47.473105 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-20 21:56:47.628144 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-20 21:56:47.776133 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-20 21:56:47.923622 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-20 21:56:48.06387 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-20 21:56:48.214571 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-20 21:56:48.348024 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-20 21:56:48.50824 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-20 21:56:48.668348 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-20 21:56:48.818537 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-20 21:56:48.957503 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-20 21:56:49.105349 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-20 21:56:49.25455 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-20 21:56:49.404493 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-20 21:56:49.543127 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-20 21:56:49.674002 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-20 21:56:49.803305 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-20 21:56:49.941282 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-20 21:56:50.089562 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-20 21:56:50.257178 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-20 21:56:50.420788 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-20 21:56:50.563729 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-20 21:56:50.703686 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-20 21:56:50.862036 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-20 21:56:51.03281 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-20 21:56:51.184361 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-20 21:56:51.337223 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-20 21:56:51.478726 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-20 21:56:51.635515 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-20 21:56:51.760756 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-20 21:56:51.917685 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-20 21:56:52.074394 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-20 21:56:52.22511 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-20 21:56:52.377358 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-20 21:56:52.537955 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-20 21:56:52.677788 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-20 21:56:52.846328 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-20 21:56:52.980689 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-20 21:56:53.135281 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-20 21:56:53.284208 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-20 21:56:53.439795 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-20 21:56:53.580335 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-20 21:56:53.723489 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-20 21:56:53.868741 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-20 21:56:54.017393 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-20 21:56:54.164385 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-20 21:56:54.315038 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-20 21:56:54.46179 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-20 21:56:54.610239 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-20 21:56:54.742275 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-20 21:56:54.900264 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-20 21:56:55.04929 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-20 21:56:55.208528 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-20 21:56:55.361485 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-20 21:56:55.486863 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-20 21:56:55.639546 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-20 21:56:55.791664 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-20 21:56:55.945491 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-20 21:56:56.091672 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-20 21:56:56.254924 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-20 21:56:56.314188 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-20 21:56:56.472101 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-20 21:56:56.639548 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-20 21:56:56.802258 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-20 21:56:56.978097 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-20 21:56:57.137784 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-20 21:56:57.298387 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-20 21:56:57.455742 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-20 21:56:57.636612 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-20 21:56:57.796544 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-20 21:56:57.948932 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-20 21:56:58.1013 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-20 21:56:58.260639 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-20 21:56:58.410706 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-20 21:56:58.566932 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-20 21:56:58.726662 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-20 21:56:58.90761 INFO::Counting total values for each feature
2025-03-20 21:56:58.933786 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-20 21:56:59.054569 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-20 21:56:59.177564 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-20 21:56:59.333855 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-20 21:56:59.411785 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-20 21:56:59.48931 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-20 21:56:59.49646 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-20 21:56:59.502965 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 32.657   0.725  33.587

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin297.104 1.88799.819