Multiple platform build/check report for BioC 3.21 - CHECK results for Maaslin2 on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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*

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: 2025-02-05 21:21:54 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 21:24:49 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 174.5 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) (2025-01-22 r87618)
* using platform: x86_64-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 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 94.286  1.793  96.848
* 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’ ...
** this is package ‘Maaslin2’ version ‘1.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 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"
2025-02-05 21:24:09.700935 INFO::Writing function arguments to log file
2025-02-05 21:24:09.762238 INFO::Verifying options selected are valid
2025-02-05 21:24:09.804391 INFO::Determining format of input files
2025-02-05 21:24:09.806418 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 21:24:09.812785 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-05 21:24:09.8143 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-05 21:24:09.817955 INFO::Filter data based on min abundance and min prevalence
2025-02-05 21:24:09.819045 INFO::Total samples in data: 1595
2025-02-05 21:24:09.820234 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-05 21:24:09.83651 INFO::Total filtered features: 0
2025-02-05 21:24:09.838269 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 21:24:09.8489 INFO::Total filtered features with variance filtering: 0
2025-02-05 21:24:09.850427 INFO::Filtered feature names from variance filtering:
2025-02-05 21:24:09.851663 INFO::Running selected normalization method: TSS
2025-02-05 21:24:11.053586 INFO::Bypass z-score application to metadata
2025-02-05 21:24:11.055076 INFO::Running selected transform method: AST
2025-02-05 21:24:11.075803 INFO::Running selected analysis method: LM
2025-02-05 21:24:11.64908 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-05 21:24:12.056029 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-05 21:24:12.262117 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-05 21:24:12.432944 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-05 21:24:12.614589 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-05 21:24:12.785576 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-05 21:24:12.955305 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-05 21:24:13.108265 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-05 21:24:13.281788 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-05 21:24:13.43243 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-05 21:24:13.574486 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-05 21:24:13.770504 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-05 21:24:13.912781 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-05 21:24:14.055111 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-05 21:24:14.223715 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-05 21:24:14.38947 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-05 21:24:14.567055 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-05 21:24:14.751773 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-05 21:24:14.910695 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-05 21:24:15.062181 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-05 21:24:15.215273 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-05 21:24:15.38145 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-05 21:24:15.545773 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-05 21:24:15.701646 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-05 21:24:15.857372 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-05 21:24:16.001574 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-05 21:24:16.164882 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-05 21:24:16.322977 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-05 21:24:16.492085 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-05 21:24:16.654073 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-05 21:24:16.809453 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-05 21:24:16.966083 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-05 21:24:17.129676 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-05 21:24:17.305746 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-05 21:24:17.476597 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-05 21:24:17.622955 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-05 21:24:17.788065 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-05 21:24:17.955953 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-05 21:24:18.12155 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-05 21:24:18.518455 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-05 21:24:18.676935 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-05 21:24:18.835733 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-05 21:24:19.008219 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-05 21:24:19.172593 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-05 21:24:19.321959 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-05 21:24:19.469498 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-05 21:24:19.642328 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-05 21:24:19.79963 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-05 21:24:19.963614 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-05 21:24:20.126916 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-05 21:24:20.274838 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-05 21:24:20.429463 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-05 21:24:20.598531 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-05 21:24:20.757964 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-05 21:24:20.927298 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-05 21:24:21.083162 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-05 21:24:21.238823 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-05 21:24:21.392111 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-05 21:24:21.532711 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-05 21:24:21.687612 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-05 21:24:21.831589 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-05 21:24:22.005987 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-05 21:24:22.154192 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-05 21:24:22.313448 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-05 21:24:22.468913 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-05 21:24:22.614897 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-05 21:24:22.768712 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-05 21:24:22.940885 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-05 21:24:23.081624 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-05 21:24:23.236654 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-05 21:24:23.41997 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-05 21:24:23.584128 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-05 21:24:23.727108 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-05 21:24:23.882604 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-05 21:24:24.025595 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-05 21:24:24.18312 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-05 21:24:24.340491 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-05 21:24:24.492285 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-05 21:24:24.644109 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-05 21:24:24.807343 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-05 21:24:24.965671 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-05 21:24:25.113686 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-05 21:24:25.267872 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-05 21:24:25.409472 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-05 21:24:25.555519 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-05 21:24:25.708343 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-05 21:24:25.863428 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-05 21:24:26.006721 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-05 21:24:26.203604 INFO::Counting total values for each feature
2025-02-05 21:24:26.239333 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-05 21:24:26.365496 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-05 21:24:26.504589 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-05 21:24:26.654799 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-05 21:24:26.705361 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-05 21:24:26.730593 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-05 21:24:26.738078 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-05 21:24:26.745299 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"
2025-02-05 21:24:26.758791 INFO::Writing function arguments to log file
2025-02-05 21:24:26.766856 INFO::Verifying options selected are valid
2025-02-05 21:24:26.767981 INFO::Determining format of input files
2025-02-05 21:24:26.769329 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 21:24:26.775766 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-05 21:24:26.777046 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-05 21:24:26.778543 INFO::Filter data based on min abundance and min prevalence
2025-02-05 21:24:26.779445 INFO::Total samples in data: 1595
2025-02-05 21:24:26.780333 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-05 21:24:26.792636 INFO::Total filtered features: 0
2025-02-05 21:24:26.79447 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 21:24:26.801455 INFO::Total filtered features with variance filtering: 0
2025-02-05 21:24:26.803458 INFO::Filtered feature names from variance filtering:
2025-02-05 21:24:26.804768 INFO::Running selected normalization method: NONE
2025-02-05 21:24:26.806079 INFO::Bypass z-score application to metadata
2025-02-05 21:24:26.807076 INFO::Running selected transform method: AST
2025-02-05 21:24:26.822121 INFO::Running selected analysis method: LM
2025-02-05 21:24:26.824386 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-05 21:24:26.975275 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-05 21:24:27.119904 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-05 21:24:27.26337 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-05 21:24:27.414924 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-05 21:24:27.555288 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-05 21:24:27.712137 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-05 21:24:27.862323 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-05 21:24:28.030538 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-05 21:24:28.168415 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-05 21:24:28.304347 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-05 21:24:28.463677 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-05 21:24:28.605504 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-05 21:24:28.730638 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-05 21:24:28.914804 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-05 21:24:29.070206 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-05 21:24:29.223377 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-05 21:24:29.396701 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-05 21:24:29.554463 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-05 21:24:29.714481 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-05 21:24:29.845058 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-05 21:24:29.995099 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-05 21:24:30.155983 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-05 21:24:30.302488 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-05 21:24:30.465161 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-05 21:24:30.620514 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-05 21:24:30.77265 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-05 21:24:30.93562 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-05 21:24:31.091722 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-05 21:24:31.234925 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-05 21:24:31.381047 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-05 21:24:31.523614 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-05 21:24:31.683336 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-05 21:24:31.848887 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-05 21:24:32.005044 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-05 21:24:32.159789 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-05 21:24:32.312987 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-05 21:24:32.458628 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-05 21:24:32.613196 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-05 21:24:32.74551 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-05 21:24:32.887761 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-05 21:24:33.035709 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-05 21:24:33.18012 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-05 21:24:33.333087 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-05 21:24:33.472681 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-05 21:24:33.617068 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-05 21:24:33.758228 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-05 21:24:33.922848 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-05 21:24:34.045561 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-05 21:24:34.19058 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-05 21:24:34.324453 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-05 21:24:34.472488 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-05 21:24:34.62007 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-05 21:24:34.759415 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-05 21:24:34.903462 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-05 21:24:35.040152 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-05 21:24:35.189008 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-05 21:24:35.329044 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-05 21:24:35.468747 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-05 21:24:35.624008 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-05 21:24:35.772005 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-05 21:24:35.929756 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-05 21:24:36.062183 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-05 21:24:36.1958 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-05 21:24:36.348708 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-05 21:24:36.48217 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-05 21:24:36.63254 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-05 21:24:36.77316 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-05 21:24:36.888433 WARNING::Fitting problem for feature 67 a warning was issued
2025-02-05 21:24:37.038183 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-05 21:24:37.168252 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-05 21:24:37.309644 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-05 21:24:37.456804 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-05 21:24:37.599933 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-05 21:24:37.65081 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-05 21:24:37.799197 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-05 21:24:37.961794 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-05 21:24:38.111611 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-05 21:24:38.260878 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-05 21:24:38.398627 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-05 21:24:38.542925 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-05 21:24:38.710871 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-05 21:24:38.860198 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-05 21:24:39.018617 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-05 21:24:39.187802 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-05 21:24:39.344111 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-05 21:24:39.505986 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-05 21:24:39.664283 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-05 21:24:39.826583 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-05 21:24:39.983783 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-05 21:24:40.182185 INFO::Counting total values for each feature
2025-02-05 21:24:40.20668 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-05 21:24:40.32985 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-05 21:24:40.460977 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-05 21:24:40.625939 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-05 21:24:40.705263 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-05 21:24:40.781219 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-05 21:24:40.788144 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-05 21:24:40.795617 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 
 31.647   0.678  32.513

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	94.286	1.793	96.848