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This page was generated on 2025-01-11 11:43 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 1126/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 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 -0500 (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 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on lconway

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: 2025-01-10 21:20:44 -0500 (Fri, 10 Jan 2025)
EndedAt: 2025-01-10 21:23:43 -0500 (Fri, 10 Jan 2025)
EllapsedTime: 178.8 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) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* 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 95.1  1.957  98.253
* 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-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.15
Current TMB package version is 1.9.16
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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-01-10 21:23:03.368189 INFO::Writing function arguments to log file
2025-01-10 21:23:03.423914 INFO::Verifying options selected are valid
2025-01-10 21:23:03.461524 INFO::Determining format of input files
2025-01-10 21:23:03.463555 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-10 21:23:03.469654 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-10 21:23:03.471234 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-10 21:23:03.474145 INFO::Filter data based on min abundance and min prevalence
2025-01-10 21:23:03.475364 INFO::Total samples in data: 1595
2025-01-10 21:23:03.476867 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-10 21:23:03.483123 INFO::Total filtered features: 0
2025-01-10 21:23:03.484927 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-10 21:23:03.504093 INFO::Total filtered features with variance filtering: 0
2025-01-10 21:23:03.505517 INFO::Filtered feature names from variance filtering:
2025-01-10 21:23:03.506861 INFO::Running selected normalization method: TSS
2025-01-10 21:23:04.808421 INFO::Bypass z-score application to metadata
2025-01-10 21:23:04.810074 INFO::Running selected transform method: AST
2025-01-10 21:23:04.830781 INFO::Running selected analysis method: LM
2025-01-10 21:23:05.487645 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-10 21:23:05.913174 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-10 21:23:06.076158 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-10 21:23:06.244084 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-10 21:23:06.418386 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-10 21:23:06.593469 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-10 21:23:06.752363 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-10 21:23:06.907978 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-10 21:23:07.058051 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-10 21:23:07.202417 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-10 21:23:07.339318 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-10 21:23:07.509526 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-10 21:23:07.827099 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-10 21:23:07.954825 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-10 21:23:08.127002 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-10 21:23:08.312481 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-10 21:23:08.472917 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-10 21:23:08.641836 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-10 21:23:08.83895 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-10 21:23:09.020212 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-10 21:23:09.185091 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-10 21:23:09.367845 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-10 21:23:09.545181 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-10 21:23:09.708482 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-10 21:23:09.866153 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-10 21:23:10.033905 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-10 21:23:10.208258 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-10 21:23:10.365224 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-10 21:23:10.534692 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-10 21:23:10.704882 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-10 21:23:10.86699 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-10 21:23:11.039902 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-10 21:23:11.199873 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-10 21:23:11.35666 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-10 21:23:11.526427 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-10 21:23:11.674085 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-10 21:23:11.823869 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-10 21:23:11.994439 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-10 21:23:12.165285 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-10 21:23:12.344199 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-10 21:23:12.521658 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-10 21:23:12.68786 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-10 21:23:12.843438 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-10 21:23:13.011237 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-10 21:23:13.183514 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-10 21:23:13.316366 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-10 21:23:13.476634 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-10 21:23:13.628153 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-10 21:23:13.810922 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-10 21:23:13.959318 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-10 21:23:14.114377 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-10 21:23:14.266716 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-10 21:23:14.418652 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-10 21:23:14.573188 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-10 21:23:14.737627 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-10 21:23:14.893582 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-10 21:23:15.052534 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-10 21:23:15.233235 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-10 21:23:15.363351 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-10 21:23:15.530488 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-10 21:23:15.670227 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-10 21:23:15.822977 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-10 21:23:15.974404 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-10 21:23:16.132288 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-10 21:23:16.294944 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-10 21:23:16.452823 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-10 21:23:16.615987 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-10 21:23:16.769341 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-10 21:23:16.922825 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-10 21:23:17.321438 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-10 21:23:17.476402 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-10 21:23:17.628541 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-10 21:23:17.787618 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-10 21:23:17.921194 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-10 21:23:18.064612 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-10 21:23:18.214909 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-10 21:23:18.374083 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-10 21:23:18.524773 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-10 21:23:18.677424 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-10 21:23:18.82675 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-10 21:23:18.983243 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-10 21:23:19.138252 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-10 21:23:19.291121 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-10 21:23:19.432783 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-10 21:23:19.577191 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-10 21:23:19.723394 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-10 21:23:19.873725 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-10 21:23:20.04052 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-10 21:23:20.252729 INFO::Counting total values for each feature
2025-01-10 21:23:20.293018 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-10 21:23:20.412589 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-10 21:23:20.561975 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-10 21:23:20.731092 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-10 21:23:20.78802 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-10 21:23:20.819429 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-10 21:23:20.825456 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-10 21:23:20.833372 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"
2025-01-10 21:23:20.850687 INFO::Writing function arguments to log file
2025-01-10 21:23:20.860123 INFO::Verifying options selected are valid
2025-01-10 21:23:20.861352 INFO::Determining format of input files
2025-01-10 21:23:20.863332 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-10 21:23:20.871076 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-10 21:23:20.872948 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-10 21:23:20.87546 INFO::Filter data based on min abundance and min prevalence
2025-01-10 21:23:20.876868 INFO::Total samples in data: 1595
2025-01-10 21:23:20.877842 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-10 21:23:20.881251 INFO::Total filtered features: 0
2025-01-10 21:23:20.882822 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-10 21:23:20.892261 INFO::Total filtered features with variance filtering: 0
2025-01-10 21:23:20.894042 INFO::Filtered feature names from variance filtering:
2025-01-10 21:23:20.895435 INFO::Running selected normalization method: NONE
2025-01-10 21:23:20.896679 INFO::Bypass z-score application to metadata
2025-01-10 21:23:20.897905 INFO::Running selected transform method: AST
2025-01-10 21:23:20.925447 INFO::Running selected analysis method: LM
2025-01-10 21:23:20.927778 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-10 21:23:21.091284 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-10 21:23:21.249637 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-10 21:23:21.409725 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-10 21:23:21.555463 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-10 21:23:21.696086 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-10 21:23:21.848862 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-10 21:23:22.011866 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-10 21:23:22.159446 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-10 21:23:22.307553 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-10 21:23:22.461531 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-10 21:23:22.612174 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-10 21:23:22.769047 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-10 21:23:22.900137 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-10 21:23:23.059613 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-10 21:23:23.206028 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-10 21:23:23.344867 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-10 21:23:23.489362 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-10 21:23:23.650866 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-10 21:23:23.800293 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-10 21:23:23.952348 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-10 21:23:24.104201 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-10 21:23:24.252244 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-10 21:23:24.413225 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-10 21:23:24.549275 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-10 21:23:24.698647 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-10 21:23:24.85919 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-10 21:23:25.003419 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-10 21:23:25.170923 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-10 21:23:25.32476 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-10 21:23:25.473255 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-10 21:23:25.620536 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-10 21:23:25.790269 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-10 21:23:25.953883 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-10 21:23:26.113897 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-10 21:23:26.268457 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-10 21:23:26.431709 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-10 21:23:26.586552 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-10 21:23:26.730249 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-10 21:23:26.898832 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-10 21:23:27.03492 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-10 21:23:27.1812 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-10 21:23:27.341067 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-10 21:23:27.484783 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-10 21:23:27.66768 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-10 21:23:27.808451 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-10 21:23:27.970779 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-10 21:23:28.129996 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-10 21:23:28.264106 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-10 21:23:28.411562 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-10 21:23:28.547321 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-10 21:23:28.676742 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-10 21:23:28.816685 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-10 21:23:28.950064 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-10 21:23:29.092199 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-10 21:23:29.249889 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-10 21:23:29.370005 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-10 21:23:29.515866 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-10 21:23:29.662649 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-10 21:23:29.810887 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-10 21:23:29.976124 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-10 21:23:30.107171 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-10 21:23:30.2445 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-10 21:23:30.406902 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-10 21:23:30.546826 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-10 21:23:30.708654 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-10 21:23:30.846113 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-10 21:23:30.994556 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-10 21:23:31.141285 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-10 21:23:31.30161 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-10 21:23:31.45783 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-10 21:23:31.59656 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-10 21:23:31.76713 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-10 21:23:31.918499 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-10 21:23:31.985205 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-10 21:23:32.138965 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-10 21:23:32.297254 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-10 21:23:32.434108 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-10 21:23:32.595696 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-10 21:23:32.748708 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-10 21:23:32.900398 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-10 21:23:33.059214 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-10 21:23:33.21912 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-10 21:23:33.381401 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-10 21:23:33.565091 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-10 21:23:33.712461 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-10 21:23:34.109957 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-10 21:23:34.262768 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-10 21:23:34.407764 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-10 21:23:34.56122 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-10 21:23:34.75205 INFO::Counting total values for each feature
2025-01-10 21:23:34.776791 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-10 21:23:34.890708 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-10 21:23:35.011898 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-10 21:23:35.158824 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-10 21:23:35.227961 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-10 21:23:35.298176 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-10 21:23:35.304503 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-10 21:23:35.313012 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 
 32.306   0.691  33.367

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin295.100 1.95798.253