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This page was generated on 2025-03-10 12:11 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (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 kjohnson1

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: 2025-03-08 00:06:49 -0500 (Sat, 08 Mar 2025)
EndedAt: 2025-03-08 00:09:40 -0500 (Sat, 08 Mar 2025)
EllapsedTime: 170.7 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: aarch64-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 Ventura 13.7.1
* 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 90.877  1.711  92.971
* 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-arm64/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 1.9.16
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: aarch64-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"
2025-03-08 00:08:55.55241 INFO::Writing function arguments to log file
2025-03-08 00:08:55.603074 INFO::Verifying options selected are valid
2025-03-08 00:08:55.644108 INFO::Determining format of input files
2025-03-08 00:08:55.646343 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-08 00:08:55.653647 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-08 00:08:55.655822 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-08 00:08:55.659012 INFO::Filter data based on min abundance and min prevalence
2025-03-08 00:08:55.660514 INFO::Total samples in data: 1595
2025-03-08 00:08:55.661796 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-08 00:08:55.667515 INFO::Total filtered features: 0
2025-03-08 00:08:55.669029 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-08 00:08:55.686289 INFO::Total filtered features with variance filtering: 0
2025-03-08 00:08:55.687839 INFO::Filtered feature names from variance filtering:
2025-03-08 00:08:55.688822 INFO::Running selected normalization method: TSS
2025-03-08 00:08:57.012657 INFO::Bypass z-score application to metadata
2025-03-08 00:08:57.014294 INFO::Running selected transform method: AST
2025-03-08 00:08:57.032748 INFO::Running selected analysis method: LM
2025-03-08 00:08:57.6759 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-08 00:08:58.099294 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-08 00:08:58.283557 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-08 00:08:58.461501 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-08 00:08:58.651823 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-08 00:08:58.828564 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-08 00:08:59.003852 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-08 00:08:59.187309 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-08 00:08:59.323505 WARNING::Fitting problem for feature 8 a warning was issued
2025-03-08 00:08:59.512937 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-08 00:08:59.658293 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-08 00:08:59.861766 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-08 00:09:00.033719 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-08 00:09:00.212712 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-08 00:09:00.427109 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-08 00:09:00.60263 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-08 00:09:00.774514 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-08 00:09:00.955093 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-08 00:09:01.142965 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-08 00:09:01.319812 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-08 00:09:01.49697 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-08 00:09:01.957536 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-08 00:09:02.127484 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-08 00:09:02.306433 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-08 00:09:02.506905 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-08 00:09:02.671174 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-08 00:09:02.842251 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-08 00:09:03.018864 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-08 00:09:03.199183 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-08 00:09:03.378115 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-08 00:09:03.55815 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-08 00:09:03.752012 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-08 00:09:03.916954 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-08 00:09:04.092715 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-08 00:09:04.272386 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-08 00:09:04.450379 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-08 00:09:04.622266 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-08 00:09:04.803311 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-08 00:09:04.97536 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-08 00:09:05.152772 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-08 00:09:05.335599 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-08 00:09:05.503726 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-08 00:09:05.677633 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-08 00:09:05.857134 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-08 00:09:06.035003 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-08 00:09:06.212682 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-08 00:09:06.391615 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-08 00:09:06.564965 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-08 00:09:06.751276 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-08 00:09:06.929618 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-08 00:09:07.095271 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-08 00:09:07.272646 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-08 00:09:07.434543 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-08 00:09:07.610299 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-08 00:09:07.776473 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-08 00:09:07.960113 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-08 00:09:08.118091 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-08 00:09:08.591335 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-08 00:09:08.772929 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-08 00:09:08.931595 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-08 00:09:09.108242 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-08 00:09:09.291705 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-08 00:09:09.459141 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-08 00:09:09.634853 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-08 00:09:10.102459 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-08 00:09:10.272641 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-08 00:09:10.444495 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-08 00:09:10.623089 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-08 00:09:10.787095 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-08 00:09:10.942026 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-08 00:09:11.12522 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-08 00:09:11.305052 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-08 00:09:11.48317 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-08 00:09:11.656627 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-08 00:09:11.845543 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-08 00:09:12.021736 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-08 00:09:12.197401 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-08 00:09:12.380526 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-08 00:09:12.553674 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-08 00:09:12.728768 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-08 00:09:12.921233 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-08 00:09:13.098001 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-08 00:09:13.266624 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-08 00:09:13.453793 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-08 00:09:13.6275 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-08 00:09:14.094828 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-08 00:09:14.26419 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-08 00:09:14.426253 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-08 00:09:14.589252 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-08 00:09:14.842563 INFO::Counting total values for each feature
2025-03-08 00:09:14.879784 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-08 00:09:15.026983 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-08 00:09:15.199219 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-08 00:09:15.372449 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-08 00:09:15.453656 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-08 00:09:15.498508 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-08 00:09:15.507724 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-08 00:09:15.516199 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"
2025-03-08 00:09:15.531268 INFO::Writing function arguments to log file
2025-03-08 00:09:15.537556 INFO::Verifying options selected are valid
2025-03-08 00:09:15.538571 INFO::Determining format of input files
2025-03-08 00:09:15.539718 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-08 00:09:15.545679 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-08 00:09:15.546886 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-08 00:09:15.548516 INFO::Filter data based on min abundance and min prevalence
2025-03-08 00:09:15.549414 INFO::Total samples in data: 1595
2025-03-08 00:09:15.550221 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-08 00:09:15.554884 INFO::Total filtered features: 0
2025-03-08 00:09:15.556006 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-08 00:09:15.564984 INFO::Total filtered features with variance filtering: 0
2025-03-08 00:09:15.566125 INFO::Filtered feature names from variance filtering:
2025-03-08 00:09:15.566915 INFO::Running selected normalization method: NONE
2025-03-08 00:09:15.567685 INFO::Bypass z-score application to metadata
2025-03-08 00:09:15.568481 INFO::Running selected transform method: AST
2025-03-08 00:09:15.586642 INFO::Running selected analysis method: LM
2025-03-08 00:09:15.588612 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-08 00:09:15.77261 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-08 00:09:15.937674 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-08 00:09:16.096473 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-08 00:09:16.279423 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-08 00:09:16.471122 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-08 00:09:16.63455 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-08 00:09:16.719521 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-08 00:09:16.832648 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-08 00:09:16.938313 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-08 00:09:17.08667 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-08 00:09:17.165778 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-08 00:09:17.27376 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-08 00:09:17.438112 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-08 00:09:17.591018 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-08 00:09:17.760596 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-08 00:09:17.925255 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-08 00:09:18.093517 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-08 00:09:18.22792 WARNING::Fitting problem for feature 16 a warning was issued
2025-03-08 00:09:18.405581 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-08 00:09:18.575325 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-08 00:09:18.742942 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-08 00:09:18.900977 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-08 00:09:19.085655 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-08 00:09:19.251904 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-08 00:09:19.421793 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-08 00:09:19.583775 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-08 00:09:19.764724 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-08 00:09:19.936649 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-08 00:09:20.098189 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-08 00:09:20.266921 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-08 00:09:20.433529 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-08 00:09:20.591179 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-08 00:09:20.758247 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-08 00:09:20.922698 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-08 00:09:21.101691 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-08 00:09:21.264801 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-08 00:09:21.4322 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-08 00:09:21.607627 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-08 00:09:21.772935 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-08 00:09:21.940991 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-08 00:09:22.109582 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-08 00:09:22.277174 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-08 00:09:22.436583 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-08 00:09:22.602393 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-08 00:09:22.780072 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-08 00:09:22.942874 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-08 00:09:23.109463 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-08 00:09:23.274704 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-08 00:09:23.45531 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-08 00:09:23.614307 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-08 00:09:23.78324 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-08 00:09:23.964731 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-08 00:09:24.121023 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-08 00:09:24.297674 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-08 00:09:24.461656 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-08 00:09:24.582723 WARNING::Fitting problem for feature 53 a warning was issued
2025-03-08 00:09:24.741933 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-08 00:09:24.90819 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-08 00:09:25.069422 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-08 00:09:25.23695 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-08 00:09:25.407767 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-08 00:09:25.568363 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-08 00:09:25.73651 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-08 00:09:25.90856 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-08 00:09:26.07076 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-08 00:09:26.241933 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-08 00:09:26.404587 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-08 00:09:26.569081 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-08 00:09:26.744549 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-08 00:09:26.917675 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-08 00:09:27.077704 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-08 00:09:27.572484 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-08 00:09:27.728216 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-08 00:09:27.896189 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-08 00:09:28.069453 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-08 00:09:28.243693 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-08 00:09:28.30186 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-08 00:09:28.462005 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-08 00:09:28.62724 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-08 00:09:28.793492 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-08 00:09:28.969267 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-08 00:09:29.138617 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-08 00:09:29.299135 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-08 00:09:29.463955 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-08 00:09:29.641724 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-08 00:09:29.79993 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-08 00:09:29.971004 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-08 00:09:30.129964 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-08 00:09:30.298287 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-08 00:09:30.4554 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-08 00:09:30.619765 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-08 00:09:30.795624 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-08 00:09:31.000438 INFO::Counting total values for each feature
2025-03-08 00:09:31.026821 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-08 00:09:31.173728 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-08 00:09:31.319418 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-08 00:09:31.493022 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-08 00:09:31.60238 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-08 00:09:31.707717 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-08 00:09:31.716951 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-08 00:09:31.72362 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 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 36.542   0.879  37.524

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin290.877 1.71192.971