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This page was generated on 2025-01-11 11:45 -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 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: 2025-01-10 20:00:25 -0500 (Fri, 10 Jan 2025)
EndedAt: 2025-01-10 20:01:23 -0500 (Fri, 10 Jan 2025)
EllapsedTime: 57.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.21.0.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: 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 ‘1.21.0’
* 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 29.031   0.57  29.769
* 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’ ...
** 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: 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"
2025-01-10 20:01:09.148524 INFO::Writing function arguments to log file
2025-01-10 20:01:09.164365 INFO::Verifying options selected are valid
2025-01-10 20:01:09.178264 INFO::Determining format of input files
2025-01-10 20:01:09.178898 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-10 20:01:09.181018 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-10 20:01:09.18147 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-10 20:01:09.182276 INFO::Filter data based on min abundance and min prevalence
2025-01-10 20:01:09.182575 INFO::Total samples in data: 1595
2025-01-10 20:01:09.182842 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-10 20:01:09.184441 INFO::Total filtered features: 0
2025-01-10 20:01:09.184782 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-10 20:01:09.191331 INFO::Total filtered features with variance filtering: 0
2025-01-10 20:01:09.191781 INFO::Filtered feature names from variance filtering:
2025-01-10 20:01:09.192102 INFO::Running selected normalization method: TSS
2025-01-10 20:01:09.617331 INFO::Bypass z-score application to metadata
2025-01-10 20:01:09.617858 INFO::Running selected transform method: AST
2025-01-10 20:01:09.623881 INFO::Running selected analysis method: LM
2025-01-10 20:01:09.848379 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-10 20:01:09.984815 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-10 20:01:10.038987 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-10 20:01:10.093071 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-10 20:01:10.152229 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-10 20:01:10.209821 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-10 20:01:10.264128 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-10 20:01:10.324395 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-10 20:01:10.380422 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-10 20:01:10.421793 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-10 20:01:10.476119 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-10 20:01:10.530823 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-10 20:01:10.582544 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-10 20:01:10.632264 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-10 20:01:10.675402 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-10 20:01:10.75042 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-10 20:01:10.793885 WARNING::Fitting problem for feature 14 a warning was issued
2025-01-10 20:01:10.849769 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-10 20:01:10.908235 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-10 20:01:10.957021 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-10 20:01:11.009176 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-10 20:01:11.061285 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-10 20:01:11.112962 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-10 20:01:11.162269 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-10 20:01:11.215069 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-10 20:01:11.269048 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-10 20:01:11.317486 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-10 20:01:11.375448 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-10 20:01:11.434071 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-10 20:01:11.487223 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-10 20:01:11.544005 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-10 20:01:11.600111 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-10 20:01:11.654941 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-10 20:01:11.707697 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-10 20:01:11.765266 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-10 20:01:11.818622 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-10 20:01:11.872536 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-10 20:01:11.9329 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-10 20:01:11.988114 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-10 20:01:12.042056 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-10 20:01:12.099918 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-10 20:01:12.150496 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-10 20:01:12.207415 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-10 20:01:12.262459 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-10 20:01:12.315237 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-10 20:01:12.373006 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-10 20:01:12.423024 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-10 20:01:12.47498 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-10 20:01:12.525857 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-10 20:01:12.581492 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-10 20:01:12.642302 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-10 20:01:12.693562 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-10 20:01:12.747436 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-10 20:01:12.799214 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-10 20:01:12.854494 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-10 20:01:12.90986 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-10 20:01:12.96883 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-10 20:01:13.01912 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-10 20:01:13.073898 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-10 20:01:13.1279 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-10 20:01:13.178744 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-10 20:01:13.231222 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-10 20:01:13.28479 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-10 20:01:13.337406 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-10 20:01:13.38807 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-10 20:01:13.445972 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-10 20:01:13.517271 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-10 20:01:13.56768 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-10 20:01:13.620078 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-10 20:01:13.677218 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-10 20:01:13.723072 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-10 20:01:13.773338 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-10 20:01:13.827858 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-10 20:01:13.887412 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-10 20:01:13.936824 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-10 20:01:13.985836 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-10 20:01:14.038877 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-10 20:01:14.088134 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-10 20:01:14.139609 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-10 20:01:14.19488 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-10 20:01:14.246819 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-10 20:01:14.305932 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-10 20:01:14.35853 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-10 20:01:14.41007 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-10 20:01:14.473347 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-10 20:01:14.524566 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-10 20:01:14.575068 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-10 20:01:14.632205 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-10 20:01:14.683474 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-10 20:01:14.733071 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-10 20:01:14.806315 INFO::Counting total values for each feature
2025-01-10 20:01:14.819339 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-10 20:01:14.867611 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-10 20:01:14.924746 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-10 20:01:14.985275 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-10 20:01:15.012408 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-10 20:01:15.027225 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-10 20:01:15.030363 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-10 20:01:15.033167 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 20:01:15.038216 INFO::Writing function arguments to log file
2025-01-10 20:01:15.040198 INFO::Verifying options selected are valid
2025-01-10 20:01:15.0405 INFO::Determining format of input files
2025-01-10 20:01:15.040892 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-10 20:01:15.042827 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-10 20:01:15.043183 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-10 20:01:15.043708 INFO::Filter data based on min abundance and min prevalence
2025-01-10 20:01:15.043986 INFO::Total samples in data: 1595
2025-01-10 20:01:15.044262 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-10 20:01:15.045769 INFO::Total filtered features: 0
2025-01-10 20:01:15.046075 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-10 20:01:15.048768 INFO::Total filtered features with variance filtering: 0
2025-01-10 20:01:15.049067 INFO::Filtered feature names from variance filtering:
2025-01-10 20:01:15.049326 INFO::Running selected normalization method: NONE
2025-01-10 20:01:15.049572 INFO::Bypass z-score application to metadata
2025-01-10 20:01:15.049817 INFO::Running selected transform method: AST
2025-01-10 20:01:15.058128 INFO::Running selected analysis method: LM
2025-01-10 20:01:15.058907 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-10 20:01:15.109053 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-10 20:01:15.254656 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-10 20:01:15.302812 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-10 20:01:15.353291 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-10 20:01:15.403402 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-10 20:01:15.462381 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-10 20:01:15.513997 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-10 20:01:15.56227 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-10 20:01:15.611898 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-10 20:01:15.666598 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-10 20:01:15.717383 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-10 20:01:15.765247 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-10 20:01:15.921532 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-10 20:01:15.970146 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-10 20:01:16.022333 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-10 20:01:16.07512 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-10 20:01:16.135063 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-10 20:01:16.186768 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-10 20:01:16.23637 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-10 20:01:16.287321 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-10 20:01:16.341833 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-10 20:01:16.391335 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-10 20:01:16.438344 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-10 20:01:16.488557 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-10 20:01:16.54093 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-10 20:01:16.590531 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-10 20:01:16.640232 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-10 20:01:16.692074 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-10 20:01:16.73781 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-10 20:01:16.78566 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-10 20:01:16.83561 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-10 20:01:16.888251 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-10 20:01:16.934365 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-10 20:01:16.98458 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-10 20:01:17.03972 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-10 20:01:17.090333 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-10 20:01:17.142208 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-10 20:01:17.194549 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-10 20:01:17.247455 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-10 20:01:17.293469 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-10 20:01:17.343069 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-10 20:01:17.395249 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-10 20:01:17.44608 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-10 20:01:17.495962 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-10 20:01:17.545995 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-10 20:01:17.601555 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-10 20:01:17.650072 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-10 20:01:17.700635 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-10 20:01:17.849811 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-10 20:01:17.8957 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-10 20:01:17.947786 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-10 20:01:17.996282 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-10 20:01:18.040093 WARNING::Fitting problem for feature 53 a warning was issued
2025-01-10 20:01:18.08599 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-10 20:01:18.131969 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-10 20:01:18.179531 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-10 20:01:18.229027 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-10 20:01:18.287278 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-10 20:01:18.336784 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-10 20:01:18.387956 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-10 20:01:18.437767 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-10 20:01:18.490359 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-10 20:01:18.538265 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-10 20:01:18.587757 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-10 20:01:18.637163 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-10 20:01:18.687404 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-10 20:01:18.74522 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-10 20:01:18.786287 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-10 20:01:18.839216 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-10 20:01:18.887132 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-10 20:01:18.94231 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-10 20:01:18.994693 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-10 20:01:19.044052 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-10 20:01:19.061852 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-10 20:01:19.112701 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-10 20:01:19.167396 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-10 20:01:19.216675 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-10 20:01:19.266894 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-10 20:01:19.318821 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-10 20:01:19.373505 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-10 20:01:19.425305 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-10 20:01:19.476919 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-10 20:01:19.527721 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-10 20:01:19.581648 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-10 20:01:19.634858 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-10 20:01:19.681517 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-10 20:01:19.731146 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-10 20:01:19.783369 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-10 20:01:19.842553 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-10 20:01:19.913237 INFO::Counting total values for each feature
2025-01-10 20:01:19.92236 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-10 20:01:19.970769 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-10 20:01:20.018888 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-10 20:01:20.075299 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-10 20:01:20.111953 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-10 20:01:20.147241 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-10 20:01:20.150294 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-10 20:01:20.152578 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 11.154   0.300  11.486

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin229.031 0.57029.769