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This page was generated on 2025-04-02 19:28 -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 nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-03-31 23:29:11 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 23:33:10 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 239.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 83.126  0.826   83.93
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 1.9.16
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 version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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"
2025-03-31 23:31:03.045507 INFO::Writing function arguments to log file
2025-03-31 23:31:03.084643 INFO::Verifying options selected are valid
2025-03-31 23:31:03.116498 INFO::Determining format of input files
2025-03-31 23:31:03.117972 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-31 23:31:03.122727 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-31 23:31:03.123961 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-31 23:31:03.12625 INFO::Filter data based on min abundance and min prevalence
2025-03-31 23:31:03.127145 INFO::Total samples in data: 1595
2025-03-31 23:31:03.128012 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-31 23:31:03.131617 INFO::Total filtered features: 0
2025-03-31 23:31:03.132594 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-31 23:31:03.139303 INFO::Total filtered features with variance filtering: 0
2025-03-31 23:31:03.14026 INFO::Filtered feature names from variance filtering:
2025-03-31 23:31:03.147523 INFO::Running selected normalization method: TSS
2025-03-31 23:31:04.224754 INFO::Bypass z-score application to metadata
2025-03-31 23:31:04.22614 INFO::Running selected transform method: AST
2025-03-31 23:31:04.242474 INFO::Running selected analysis method: LM
2025-03-31 23:31:04.789549 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-31 23:31:05.103542 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-31 23:31:05.2609 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-31 23:31:05.401882 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-31 23:31:05.551752 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-31 23:31:05.700384 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-31 23:31:05.854283 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-31 23:31:05.995028 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-31 23:31:06.106099 WARNING::Fitting problem for feature 8 a warning was issued
2025-03-31 23:31:06.258905 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-31 23:31:06.371448 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-31 23:31:06.565295 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-31 23:31:06.702072 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-31 23:31:06.84569 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-31 23:31:06.978103 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-31 23:31:07.097709 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-31 23:31:07.242449 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-31 23:31:07.385352 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-31 23:31:07.528686 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-31 23:31:07.670026 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-31 23:31:07.812167 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-31 23:31:07.996983 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-31 23:31:08.136826 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-31 23:31:08.282396 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-31 23:31:08.430895 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-31 23:31:08.575221 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-31 23:31:08.721031 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-31 23:31:08.868448 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-31 23:31:09.011321 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-31 23:31:09.158914 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-31 23:31:09.312346 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-31 23:31:09.48551 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-31 23:31:09.63546 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-31 23:31:09.783297 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-31 23:31:09.927548 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-31 23:31:10.080117 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-31 23:31:10.226797 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-31 23:31:10.370126 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-31 23:31:10.516167 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-31 23:31:10.679421 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-31 23:31:10.832899 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-31 23:31:10.980626 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-31 23:31:11.133116 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-31 23:31:11.533353 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-31 23:31:11.678816 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-31 23:31:11.831881 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-31 23:31:11.981704 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-31 23:31:12.11378 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-31 23:31:12.261366 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-31 23:31:12.421774 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-31 23:31:12.571635 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-31 23:31:12.716745 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-31 23:31:12.879736 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-31 23:31:13.019758 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-31 23:31:13.164302 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-31 23:31:13.317446 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-31 23:31:13.477173 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-31 23:31:13.609358 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-31 23:31:13.755667 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-31 23:31:13.919335 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-31 23:31:14.053372 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-31 23:31:14.207171 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-31 23:31:14.356862 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-31 23:31:14.499931 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-31 23:31:14.647976 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-31 23:31:14.799887 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-31 23:31:14.940833 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-31 23:31:15.079848 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-31 23:31:15.234437 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-31 23:31:15.386837 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-31 23:31:15.529592 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-31 23:31:15.697416 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-31 23:31:15.853076 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-31 23:31:15.998118 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-31 23:31:16.138602 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-31 23:31:16.273348 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-31 23:31:16.42876 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-31 23:31:16.595152 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-31 23:31:16.748014 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-31 23:31:16.906693 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-31 23:31:17.04679 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-31 23:31:17.196369 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-31 23:31:17.351223 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-31 23:31:17.496263 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-31 23:31:17.65923 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-31 23:31:17.803564 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-31 23:31:17.941005 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-31 23:31:18.091048 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-31 23:31:18.227772 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-31 23:31:18.376447 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-31 23:31:18.559172 INFO::Counting total values for each feature
2025-03-31 23:31:18.599016 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-31 23:31:18.693231 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-31 23:31:18.789033 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-31 23:31:18.887061 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-31 23:31:18.93764 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-31 23:31:18.964827 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-31 23:31:18.970237 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-31 23:31:18.975612 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"
2025-03-31 23:31:18.988554 INFO::Writing function arguments to log file
2025-03-31 23:31:18.994297 INFO::Verifying options selected are valid
2025-03-31 23:31:18.995296 INFO::Determining format of input files
2025-03-31 23:31:18.996431 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-31 23:31:19.00153 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-31 23:31:19.00256 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-31 23:31:19.004161 INFO::Filter data based on min abundance and min prevalence
2025-03-31 23:31:19.005006 INFO::Total samples in data: 1595
2025-03-31 23:31:19.005836 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-31 23:31:19.020206 INFO::Total filtered features: 0
2025-03-31 23:31:19.021431 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-31 23:31:19.029087 INFO::Total filtered features with variance filtering: 0
2025-03-31 23:31:19.030136 INFO::Filtered feature names from variance filtering:
2025-03-31 23:31:19.030991 INFO::Running selected normalization method: NONE
2025-03-31 23:31:19.031815 INFO::Bypass z-score application to metadata
2025-03-31 23:31:19.032624 INFO::Running selected transform method: AST
2025-03-31 23:31:19.050924 INFO::Running selected analysis method: LM
2025-03-31 23:31:19.052743 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-31 23:31:19.200746 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-31 23:31:19.334237 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-31 23:31:19.467695 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-31 23:31:19.625617 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-31 23:31:19.760623 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-31 23:31:19.89593 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-31 23:31:20.040351 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-31 23:31:20.175386 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-31 23:31:20.313278 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-31 23:31:20.459275 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-31 23:31:20.570419 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-31 23:31:20.711314 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-31 23:31:20.850376 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-31 23:31:20.982608 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-31 23:31:21.112414 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-31 23:31:21.252879 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-31 23:31:21.356788 WARNING::Fitting problem for feature 16 a warning was issued
2025-03-31 23:31:21.498308 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-31 23:31:21.636362 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-31 23:31:21.769796 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-31 23:31:21.911078 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-31 23:31:22.04579 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-31 23:31:22.186641 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-31 23:31:22.326459 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-31 23:31:22.456345 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-31 23:31:22.594729 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-31 23:31:22.735871 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-31 23:31:22.871918 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-31 23:31:23.016734 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-31 23:31:23.150694 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-31 23:31:23.280484 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-31 23:31:23.427335 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-31 23:31:23.557507 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-31 23:31:23.696352 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-31 23:31:23.831753 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-31 23:31:23.962145 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-31 23:31:24.105319 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-31 23:31:24.240236 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-31 23:31:24.372615 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-31 23:31:24.511625 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-31 23:31:24.63626 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-31 23:31:24.772445 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-31 23:31:24.903128 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-31 23:31:25.038866 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-31 23:31:25.181976 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-31 23:31:25.325326 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-31 23:31:25.46715 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-31 23:31:25.604185 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-31 23:31:25.743551 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-31 23:31:25.875166 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-31 23:31:26.009277 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-31 23:31:26.132169 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-31 23:31:26.272936 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-31 23:31:26.411542 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-31 23:31:26.533449 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-31 23:31:26.664888 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-31 23:31:26.791339 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-31 23:31:26.928523 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-31 23:31:27.068861 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-31 23:31:27.197925 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-31 23:31:27.332035 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-31 23:31:27.468228 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-31 23:31:27.593812 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-31 23:31:27.72061 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-31 23:31:27.861756 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-31 23:31:27.990414 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-31 23:31:28.131874 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-31 23:31:28.260409 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-31 23:31:28.371023 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-31 23:31:28.51855 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-31 23:31:28.645132 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-31 23:31:28.79395 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-31 23:31:28.932385 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-31 23:31:29.067944 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-31 23:31:29.124727 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-31 23:31:29.260257 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-31 23:31:29.391781 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-31 23:31:29.534059 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-31 23:31:29.662688 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-31 23:31:29.806107 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-31 23:31:29.933512 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-31 23:31:30.064401 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-31 23:31:30.207565 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-31 23:31:30.336684 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-31 23:31:30.485227 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-31 23:31:30.613748 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-31 23:31:30.746358 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-31 23:31:30.872012 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-31 23:31:31.008767 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-31 23:31:31.143383 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-31 23:31:31.311175 INFO::Counting total values for each feature
2025-03-31 23:31:31.33257 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-31 23:31:31.425142 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-31 23:31:31.517744 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-31 23:31:31.621767 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-31 23:31:31.685071 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-31 23:31:31.746493 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-31 23:31:31.752045 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-31 23:31:31.756757 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 29.259   0.479  29.727

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin283.126 0.82683.930