Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-03-19 11:46 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1141/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on kjohnson3

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Maaslin2
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-03-18 20:02:25 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 20:03:24 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 58.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 29.796  0.617   30.62
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.16
Current TMB package version is 1.9.17
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: 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 20:03:09.961389 INFO::Writing function arguments to log file
2025-03-18 20:03:09.978369 INFO::Verifying options selected are valid
2025-03-18 20:03:09.991416 INFO::Determining format of input files
2025-03-18 20:03:09.992067 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 20:03:09.994167 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 20:03:09.994648 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-18 20:03:09.995424 INFO::Filter data based on min abundance and min prevalence
2025-03-18 20:03:09.995726 INFO::Total samples in data: 1595
2025-03-18 20:03:09.996006 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 20:03:10.000796 INFO::Total filtered features: 0
2025-03-18 20:03:10.001251 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 20:03:10.00436 INFO::Total filtered features with variance filtering: 0
2025-03-18 20:03:10.004735 INFO::Filtered feature names from variance filtering:
2025-03-18 20:03:10.005013 INFO::Running selected normalization method: TSS
2025-03-18 20:03:10.419539 INFO::Bypass z-score application to metadata
2025-03-18 20:03:10.420055 INFO::Running selected transform method: AST
2025-03-18 20:03:10.425822 INFO::Running selected analysis method: LM
2025-03-18 20:03:10.623371 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 20:03:10.747566 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 20:03:10.806769 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 20:03:10.859555 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 20:03:10.917937 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 20:03:10.97233 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 20:03:11.028722 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 20:03:11.081227 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 20:03:11.139148 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 20:03:11.181468 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-18 20:03:11.256435 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 20:03:11.308132 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 20:03:11.362077 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 20:03:11.419416 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 20:03:11.475915 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 20:03:11.533318 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 20:03:11.588388 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 20:03:11.64586 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 20:03:11.702256 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 20:03:11.761604 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 20:03:11.812931 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 20:03:11.873625 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 20:03:11.927977 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 20:03:11.984478 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 20:03:12.040499 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 20:03:12.09495 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 20:03:12.152334 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 20:03:12.202893 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 20:03:12.264971 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 20:03:12.32316 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 20:03:12.381273 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 20:03:12.432665 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 20:03:12.490221 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 20:03:12.549029 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 20:03:12.712154 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 20:03:12.762006 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 20:03:12.817071 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 20:03:12.874897 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 20:03:12.92777 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 20:03:12.977681 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 20:03:13.033359 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 20:03:13.086839 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 20:03:13.13991 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 20:03:13.199727 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 20:03:13.250969 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 20:03:13.302898 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 20:03:13.359814 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 20:03:13.412691 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 20:03:13.468271 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 20:03:13.523101 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 20:03:13.573383 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 20:03:13.625473 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 20:03:13.680272 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 20:03:13.732645 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 20:03:13.791856 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 20:03:13.842063 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 20:03:13.896523 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 20:03:13.957726 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 20:03:14.007344 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 20:03:14.061646 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 20:03:14.120497 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 20:03:14.171765 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 20:03:14.22662 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 20:03:14.284297 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 20:03:14.33567 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 20:03:14.387028 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 20:03:14.443304 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 20:03:14.4955 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 20:03:14.544376 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 20:03:14.603504 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 20:03:14.657413 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 20:03:14.712358 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 20:03:14.767333 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 20:03:14.817335 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 20:03:14.872858 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 20:03:14.923664 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 20:03:14.976217 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 20:03:15.03297 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 20:03:15.084247 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 20:03:15.144262 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 20:03:15.19781 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 20:03:15.248374 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 20:03:15.305359 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 20:03:15.357413 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 20:03:15.411568 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 20:03:15.464657 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 20:03:15.526439 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 20:03:15.579758 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 20:03:15.652602 INFO::Counting total values for each feature
2025-03-18 20:03:15.666065 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-18 20:03:15.714334 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-18 20:03:15.770759 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-18 20:03:15.830936 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-18 20:03:15.858701 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-18 20:03:15.873884 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-18 20:03:15.876824 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-18 20:03:15.879489 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 20:03:15.884328 INFO::Writing function arguments to log file
2025-03-18 20:03:15.886255 INFO::Verifying options selected are valid
2025-03-18 20:03:15.886555 INFO::Determining format of input files
2025-03-18 20:03:15.886944 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 20:03:15.88884 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 20:03:15.889184 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-18 20:03:15.889686 INFO::Filter data based on min abundance and min prevalence
2025-03-18 20:03:15.889965 INFO::Total samples in data: 1595
2025-03-18 20:03:15.890226 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 20:03:15.891707 INFO::Total filtered features: 0
2025-03-18 20:03:15.892016 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 20:03:15.8948 INFO::Total filtered features with variance filtering: 0
2025-03-18 20:03:15.895132 INFO::Filtered feature names from variance filtering:
2025-03-18 20:03:15.895399 INFO::Running selected normalization method: NONE
2025-03-18 20:03:15.895641 INFO::Bypass z-score application to metadata
2025-03-18 20:03:15.895884 INFO::Running selected transform method: AST
2025-03-18 20:03:15.903881 INFO::Running selected analysis method: LM
2025-03-18 20:03:15.90463 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 20:03:16.064274 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 20:03:16.115836 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 20:03:16.164641 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 20:03:16.223894 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 20:03:16.278505 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 20:03:16.332267 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 20:03:16.384218 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 20:03:16.438801 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 20:03:16.491419 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 20:03:16.544988 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 20:03:16.5894 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-18 20:03:16.651175 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 20:03:16.701432 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 20:03:16.746175 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 20:03:16.803487 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 20:03:16.858514 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 20:03:16.909737 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 20:03:16.95841 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 20:03:17.01571 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 20:03:17.065494 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 20:03:17.113938 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 20:03:17.163719 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 20:03:17.21891 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 20:03:17.273011 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 20:03:17.321914 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 20:03:17.379674 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 20:03:17.431175 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 20:03:17.483706 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 20:03:17.543526 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 20:03:17.594856 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 20:03:17.644968 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 20:03:17.698382 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 20:03:17.763862 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 20:03:17.816998 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 20:03:17.870459 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 20:03:17.931106 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 20:03:17.988202 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 20:03:18.039285 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 20:03:18.090746 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 20:03:18.146592 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 20:03:18.194776 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 20:03:18.243127 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 20:03:18.293141 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 20:03:18.349486 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 20:03:18.401836 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 20:03:18.454949 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 20:03:18.510225 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 20:03:18.563582 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 20:03:18.614737 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 20:03:18.669772 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 20:03:18.719729 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 20:03:18.767709 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 20:03:18.827887 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 20:03:18.876276 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 20:03:18.923604 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 20:03:18.978569 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 20:03:19.027445 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 20:03:19.077756 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 20:03:19.131697 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 20:03:19.181162 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 20:03:19.233354 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 20:03:19.286695 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 20:03:19.338247 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 20:03:19.392869 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 20:03:19.443831 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 20:03:19.494329 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 20:03:19.549217 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 20:03:19.600408 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 20:03:19.657951 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 20:03:19.710156 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 20:03:19.768297 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 20:03:19.821497 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 20:03:19.872029 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 20:03:19.89392 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-18 20:03:19.9441 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 20:03:19.998326 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 20:03:20.049877 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 20:03:20.104996 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 20:03:20.155695 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 20:03:20.208141 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 20:03:20.258721 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 20:03:20.3161 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 20:03:20.371177 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 20:03:20.425007 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 20:03:20.483459 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 20:03:20.532084 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 20:03:20.583267 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 20:03:20.642413 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 20:03:20.695209 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 20:03:20.757876 INFO::Counting total values for each feature
2025-03-18 20:03:20.771402 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-18 20:03:20.819454 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-18 20:03:20.868018 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-18 20:03:20.924449 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-18 20:03:20.960635 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-18 20:03:20.995643 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-18 20:03:20.998761 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-18 20:03:21.001066 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 
 11.145   0.307  11.470

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin229.796 0.61730.620