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This page was generated on 2025-03-20 12:10 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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: 2025-03-17 13:00 -0400 (Mon, 17 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 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: 2025-03-18 23:49:32 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 23:52:22 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 170.4 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 92.323  1.843  94.485
* 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 1.9.17
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: 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"
2025-03-18 23:51:38.668398 INFO::Writing function arguments to log file
2025-03-18 23:51:38.716165 INFO::Verifying options selected are valid
2025-03-18 23:51:38.755883 INFO::Determining format of input files
2025-03-18 23:51:38.757764 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 23:51:38.764456 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 23:51:38.76595 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-18 23:51:38.768423 INFO::Filter data based on min abundance and min prevalence
2025-03-18 23:51:38.769378 INFO::Total samples in data: 1595
2025-03-18 23:51:38.770202 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 23:51:38.775395 INFO::Total filtered features: 0
2025-03-18 23:51:38.776602 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 23:51:38.793697 INFO::Total filtered features with variance filtering: 0
2025-03-18 23:51:38.79515 INFO::Filtered feature names from variance filtering:
2025-03-18 23:51:38.796031 INFO::Running selected normalization method: TSS
2025-03-18 23:51:40.071838 INFO::Bypass z-score application to metadata
2025-03-18 23:51:40.073589 INFO::Running selected transform method: AST
2025-03-18 23:51:40.091745 INFO::Running selected analysis method: LM
2025-03-18 23:51:40.734226 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 23:51:41.15932 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 23:51:41.334154 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 23:51:41.510129 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 23:51:41.670324 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 23:51:41.757836 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 23:51:41.860285 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 23:51:41.977141 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 23:51:42.124937 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 23:51:42.246845 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-18 23:51:42.419069 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 23:51:42.575485 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 23:51:42.658843 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 23:51:42.803047 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 23:51:43.026738 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 23:51:43.201309 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 23:51:43.378364 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 23:51:43.587234 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 23:51:43.773603 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 23:51:43.948883 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 23:51:44.123333 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 23:51:44.317567 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 23:51:44.493582 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 23:51:44.669603 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 23:51:45.131219 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 23:51:45.301798 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 23:51:45.472432 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 23:51:45.633459 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 23:51:45.82007 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 23:51:45.989855 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 23:51:46.167585 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 23:51:46.348278 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 23:51:46.530233 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 23:51:46.709398 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 23:51:46.906406 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 23:51:47.066916 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 23:51:47.232666 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 23:51:47.402549 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 23:51:47.586115 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 23:51:47.747501 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 23:51:47.914455 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 23:51:48.09876 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 23:51:48.268117 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 23:51:48.443553 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 23:51:48.609037 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 23:51:48.784458 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 23:51:48.958312 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 23:51:49.42645 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 23:51:49.607399 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 23:51:49.781461 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 23:51:49.96468 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 23:51:50.129172 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 23:51:50.302081 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 23:51:50.488647 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 23:51:50.66659 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 23:51:50.829672 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 23:51:51.018284 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 23:51:51.195274 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 23:51:51.356198 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 23:51:51.544018 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 23:51:51.70712 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 23:51:51.868744 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 23:51:52.047673 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 23:51:52.221975 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 23:51:52.393925 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 23:51:52.573489 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 23:51:52.737106 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 23:51:52.909281 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 23:51:53.082356 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 23:51:53.248586 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 23:51:53.432237 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 23:51:53.624065 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 23:51:53.797262 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 23:51:53.983432 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 23:51:54.165831 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 23:51:54.34523 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 23:51:54.540884 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 23:51:54.719682 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 23:51:54.903175 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 23:51:55.090494 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 23:51:55.280891 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 23:51:55.452396 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 23:51:55.648732 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 23:51:55.821306 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 23:51:56.006725 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 23:51:56.178743 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 23:51:56.345489 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 23:51:56.527307 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 23:51:56.743594 INFO::Counting total values for each feature
2025-03-18 23:51:56.781528 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-18 23:51:56.929121 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-18 23:51:57.102209 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-18 23:51:57.275034 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-18 23:51:57.356875 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-18 23:51:57.693297 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-18 23:51:57.703054 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-18 23:51:57.711929 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"
2025-03-18 23:51:57.727514 INFO::Writing function arguments to log file
2025-03-18 23:51:57.734038 INFO::Verifying options selected are valid
2025-03-18 23:51:57.7351 INFO::Determining format of input files
2025-03-18 23:51:57.73627 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 23:51:57.741997 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 23:51:57.743298 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-18 23:51:57.745208 INFO::Filter data based on min abundance and min prevalence
2025-03-18 23:51:57.746258 INFO::Total samples in data: 1595
2025-03-18 23:51:57.747115 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 23:51:57.751762 INFO::Total filtered features: 0
2025-03-18 23:51:57.75292 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 23:51:57.761852 INFO::Total filtered features with variance filtering: 0
2025-03-18 23:51:57.763262 INFO::Filtered feature names from variance filtering:
2025-03-18 23:51:57.764434 INFO::Running selected normalization method: NONE
2025-03-18 23:51:57.765546 INFO::Bypass z-score application to metadata
2025-03-18 23:51:57.766414 INFO::Running selected transform method: AST
2025-03-18 23:51:57.783288 INFO::Running selected analysis method: LM
2025-03-18 23:51:57.785201 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 23:51:57.951729 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 23:51:58.134456 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 23:51:58.295031 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 23:51:58.461107 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 23:51:58.633363 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 23:51:58.815908 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 23:51:58.981412 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 23:51:59.145173 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 23:51:59.325886 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 23:51:59.490549 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 23:51:59.631404 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-18 23:51:59.820927 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 23:51:59.991411 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 23:52:00.127751 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 23:52:00.299575 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 23:52:00.470942 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 23:52:00.642502 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 23:52:00.807348 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 23:52:00.992304 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 23:52:01.162963 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 23:52:01.331609 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 23:52:01.519554 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 23:52:01.688998 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 23:52:01.860643 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 23:52:02.028657 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 23:52:02.196858 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 23:52:02.365047 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 23:52:02.537216 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 23:52:02.656533 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 23:52:02.812464 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 23:52:02.985294 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 23:52:03.147461 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 23:52:03.320998 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 23:52:03.484021 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 23:52:03.63988 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 23:52:03.80742 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 23:52:03.967824 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 23:52:04.137721 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 23:52:04.300839 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 23:52:04.469693 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 23:52:04.618951 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 23:52:04.782038 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 23:52:04.941549 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 23:52:05.111872 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 23:52:05.279188 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 23:52:05.450156 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 23:52:05.607718 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 23:52:05.778633 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 23:52:05.93995 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 23:52:06.101527 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 23:52:06.294771 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 23:52:06.457212 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 23:52:06.625338 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 23:52:06.799751 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 23:52:06.945829 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 23:52:07.102915 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 23:52:07.266672 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 23:52:07.437909 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 23:52:07.592839 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 23:52:07.749826 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 23:52:07.926664 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 23:52:08.077805 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 23:52:08.232358 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 23:52:08.403677 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 23:52:08.567754 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 23:52:08.727819 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 23:52:08.903496 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 23:52:09.06369 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 23:52:09.235341 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 23:52:09.411326 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 23:52:09.582298 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 23:52:09.764072 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 23:52:09.933935 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 23:52:09.990672 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-18 23:52:10.149025 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 23:52:10.328239 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 23:52:10.501512 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 23:52:10.666158 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 23:52:10.849092 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 23:52:11.011376 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 23:52:11.190284 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 23:52:11.362982 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 23:52:11.837008 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 23:52:12.012868 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 23:52:12.172086 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 23:52:12.32908 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 23:52:12.517897 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 23:52:12.676198 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 23:52:12.844783 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 23:52:13.038359 INFO::Counting total values for each feature
2025-03-18 23:52:13.066458 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-18 23:52:13.214591 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-18 23:52:13.360015 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-18 23:52:13.532121 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-18 23:52:13.642457 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-18 23:52:13.749498 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-18 23:52:13.758962 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-18 23:52:13.765939 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 
 35.560   0.751  36.454

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin292.323 1.84394.485