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This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on merida1

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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2025-04-01 05:02:15 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 05:07:48 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 333.0 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 180.33   2.72 195.068
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** 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 1.9.15
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 version 4.4.3 (2025-02-28) -- "Trophy Case"
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"
2025-04-01 05:06:32.24468 INFO::Writing function arguments to log file
2025-04-01 05:06:32.33185 INFO::Verifying options selected are valid
2025-04-01 05:06:32.404261 INFO::Determining format of input files
2025-04-01 05:06:32.407571 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 05:06:32.421426 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 05:06:32.425423 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-01 05:06:32.431623 INFO::Filter data based on min abundance and min prevalence
2025-04-01 05:06:32.434135 INFO::Total samples in data: 1595
2025-04-01 05:06:32.436457 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 05:06:32.447138 INFO::Total filtered features: 0
2025-04-01 05:06:32.449666 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 05:06:32.478888 INFO::Total filtered features with variance filtering: 0
2025-04-01 05:06:32.481517 INFO::Filtered feature names from variance filtering:
2025-04-01 05:06:32.483942 INFO::Running selected normalization method: TSS
2025-04-01 05:06:34.915207 INFO::Bypass z-score application to metadata
2025-04-01 05:06:34.917876 INFO::Running selected transform method: AST
2025-04-01 05:06:34.955873 INFO::Running selected analysis method: LM
2025-04-01 05:06:36.144551 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 05:06:36.907151 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 05:06:37.234388 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 05:06:37.570799 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 05:06:37.903483 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 05:06:38.210284 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 05:06:38.516693 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 05:06:38.83679 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 05:06:39.156709 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 05:06:39.451958 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 05:06:39.755195 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 05:06:40.102964 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 05:06:40.419983 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 05:06:40.700762 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-01 05:06:41.059696 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 05:06:41.378729 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 05:06:41.696172 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 05:06:42.019648 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 05:06:42.368751 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 05:06:42.686739 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 05:06:43.006393 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 05:06:43.345569 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 05:06:43.679007 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 05:06:44.003487 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 05:06:44.311168 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 05:06:44.638523 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 05:06:44.955005 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 05:06:45.265734 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 05:06:45.603993 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 05:06:45.92258 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 05:06:46.250055 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 05:06:46.567302 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 05:06:46.88934 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 05:06:47.215505 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 05:06:47.55705 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 05:06:47.866228 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 05:06:48.185244 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 05:06:48.512022 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 05:06:48.839702 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 05:06:49.156253 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 05:06:49.491414 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 05:06:49.823759 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 05:06:50.156356 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 05:06:50.480652 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 05:06:50.791224 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 05:06:51.11938 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 05:06:51.440501 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 05:06:51.760053 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 05:06:52.092387 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 05:06:52.395349 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 05:06:52.714563 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 05:06:53.0239 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 05:06:53.352398 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 05:06:53.669493 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 05:06:54.01749 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 05:06:54.325028 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 05:06:54.657781 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 05:06:54.999189 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 05:06:55.306996 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 05:06:55.635282 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 05:06:55.951641 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 05:06:56.320148 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 05:06:56.901621 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 05:06:57.220704 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 05:06:57.535719 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 05:06:57.849612 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 05:06:58.1648 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 05:06:58.476161 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 05:06:58.779333 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 05:06:59.105164 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 05:06:59.432197 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 05:06:59.765356 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 05:07:00.078322 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 05:07:00.374511 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 05:07:00.67959 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 05:07:00.998154 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 05:07:01.341666 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 05:07:01.683684 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 05:07:02.260869 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 05:07:02.580836 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 05:07:02.90837 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 05:07:03.294529 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 05:07:03.620972 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 05:07:03.956302 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 05:07:04.298832 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 05:07:04.615076 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 05:07:04.96421 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 05:07:05.291966 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 05:07:05.792088 INFO::Counting total values for each feature
2025-04-01 05:07:05.890126 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-01 05:07:06.182148 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-01 05:07:06.547946 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-01 05:07:06.911849 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-01 05:07:07.005079 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-01 05:07:07.065162 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-01 05:07:07.077517 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-01 05:07:07.094787 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"
2025-04-01 05:07:07.12878 INFO::Writing function arguments to log file
2025-04-01 05:07:07.14962 INFO::Verifying options selected are valid
2025-04-01 05:07:07.151709 INFO::Determining format of input files
2025-04-01 05:07:07.15486 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 05:07:07.17232 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 05:07:07.175524 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-01 05:07:07.181002 INFO::Filter data based on min abundance and min prevalence
2025-04-01 05:07:07.186362 INFO::Total samples in data: 1595
2025-04-01 05:07:07.190461 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 05:07:07.215901 INFO::Total filtered features: 0
2025-04-01 05:07:07.220226 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 05:07:07.238909 INFO::Total filtered features with variance filtering: 0
2025-04-01 05:07:07.241575 INFO::Filtered feature names from variance filtering:
2025-04-01 05:07:07.243945 INFO::Running selected normalization method: NONE
2025-04-01 05:07:07.246628 INFO::Bypass z-score application to metadata
2025-04-01 05:07:07.249685 INFO::Running selected transform method: AST
2025-04-01 05:07:07.285272 INFO::Running selected analysis method: LM
2025-04-01 05:07:07.2886 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 05:07:07.602234 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 05:07:07.903772 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 05:07:08.223973 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 05:07:08.542879 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 05:07:08.834754 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 05:07:09.127878 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 05:07:09.444101 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 05:07:09.741607 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 05:07:10.056521 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 05:07:10.359835 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 05:07:10.665451 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 05:07:10.953651 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 05:07:11.188761 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-01 05:07:11.518227 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 05:07:11.817314 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 05:07:12.189942 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 05:07:12.535069 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 05:07:12.8746 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 05:07:13.176358 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 05:07:13.476175 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 05:07:13.762062 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 05:07:14.053457 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 05:07:14.387051 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 05:07:14.691997 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 05:07:15.010058 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 05:07:15.366976 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 05:07:15.659271 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 05:07:15.963777 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 05:07:16.23979 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 05:07:16.523609 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 05:07:16.831529 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 05:07:17.138599 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 05:07:17.446345 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 05:07:17.740878 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 05:07:18.045715 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 05:07:18.352701 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 05:07:18.661944 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 05:07:18.965041 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 05:07:19.306987 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 05:07:19.599578 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 05:07:19.890751 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 05:07:20.255585 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 05:07:20.552496 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 05:07:20.852704 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 05:07:21.171607 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 05:07:21.470512 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 05:07:21.771103 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 05:07:22.074674 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 05:07:22.388844 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 05:07:22.740911 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 05:07:23.042688 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 05:07:23.343601 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 05:07:23.625583 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 05:07:23.91578 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 05:07:24.207009 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 05:07:24.495586 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 05:07:24.805811 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 05:07:25.103136 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 05:07:25.422645 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 05:07:25.726293 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 05:07:26.012589 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 05:07:26.332985 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 05:07:26.633622 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 05:07:26.931426 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 05:07:27.238686 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 05:07:27.545031 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 05:07:27.83616 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 05:07:28.084081 WARNING::Fitting problem for feature 67 a warning was issued
2025-04-01 05:07:28.396158 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 05:07:28.705737 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 05:07:29.007694 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 05:07:29.306136 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 05:07:29.604365 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 05:07:29.709959 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-01 05:07:30.029282 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 05:07:30.343158 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 05:07:30.661766 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 05:07:30.959069 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 05:07:31.27144 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 05:07:31.566403 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 05:07:31.865729 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 05:07:32.183763 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 05:07:32.495496 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 05:07:32.804426 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 05:07:33.103212 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 05:07:33.392753 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 05:07:33.697426 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 05:07:33.990563 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 05:07:34.285932 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 05:07:34.682485 INFO::Counting total values for each feature
2025-04-01 05:07:34.764956 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-01 05:07:35.062537 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-01 05:07:35.355463 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-01 05:07:35.728582 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-01 05:07:35.864942 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-01 05:07:35.986961 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-01 05:07:35.99877 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-01 05:07:36.012833 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 
 61.704   1.091  66.447

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2180.330 2.720195.068