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"	4481
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4492
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4445
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: 2025-02-12 21:24:44 -0500 (Wed, 12 Feb 2025)

EndedAt: 2025-02-12 21:27:40 -0500 (Wed, 12 Feb 2025)

EllapsedTime: 175.6 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 94.343  1.685  96.794
* 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"
2025-02-12 21:26:59.703559 INFO::Writing function arguments to log file
2025-02-12 21:26:59.758498 INFO::Verifying options selected are valid
2025-02-12 21:26:59.800194 INFO::Determining format of input files
2025-02-12 21:26:59.801808 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-12 21:26:59.809647 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-12 21:26:59.811148 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-12 21:26:59.813642 INFO::Filter data based on min abundance and min prevalence
2025-02-12 21:26:59.814776 INFO::Total samples in data: 1595
2025-02-12 21:26:59.815932 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-12 21:26:59.828503 INFO::Total filtered features: 0
2025-02-12 21:26:59.829971 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-12 21:26:59.840425 INFO::Total filtered features with variance filtering: 0
2025-02-12 21:26:59.841808 INFO::Filtered feature names from variance filtering:
2025-02-12 21:26:59.843055 INFO::Running selected normalization method: TSS
2025-02-12 21:27:01.062234 INFO::Bypass z-score application to metadata
2025-02-12 21:27:01.064049 INFO::Running selected transform method: AST
2025-02-12 21:27:01.079833 INFO::Running selected analysis method: LM
2025-02-12 21:27:01.640219 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-12 21:27:02.010318 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-12 21:27:02.174043 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-12 21:27:02.332699 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-12 21:27:02.480548 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-12 21:27:02.644797 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-12 21:27:02.806345 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-12 21:27:02.959725 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-12 21:27:03.366114 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-12 21:27:03.501913 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-12 21:27:03.632755 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-12 21:27:03.776007 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-12 21:27:03.909556 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-12 21:27:04.031286 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-12 21:27:04.194577 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-12 21:27:04.374021 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-12 21:27:04.527967 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-12 21:27:04.666881 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-12 21:27:04.834703 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-12 21:27:04.985532 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-12 21:27:05.131905 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-12 21:27:05.290626 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-12 21:27:05.451031 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-12 21:27:05.615654 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-12 21:27:05.771516 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-12 21:27:05.929183 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-12 21:27:06.087942 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-12 21:27:06.229913 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-12 21:27:06.398174 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-12 21:27:06.578709 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-12 21:27:06.741554 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-12 21:27:06.898501 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-12 21:27:07.071515 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-12 21:27:07.244322 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-12 21:27:07.423255 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-12 21:27:07.587765 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-12 21:27:07.752314 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-12 21:27:07.941616 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-12 21:27:08.099298 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-12 21:27:08.25858 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-12 21:27:08.43201 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-12 21:27:08.60486 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-12 21:27:08.776588 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-12 21:27:08.944641 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-12 21:27:09.097369 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-12 21:27:09.246892 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-12 21:27:09.424573 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-12 21:27:09.573621 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-12 21:27:09.759809 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-12 21:27:09.922158 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-12 21:27:10.081251 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-12 21:27:10.244567 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-12 21:27:10.3998 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-12 21:27:10.565087 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-12 21:27:10.733496 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-12 21:27:10.893294 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-12 21:27:11.043579 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-12 21:27:11.217723 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-12 21:27:11.362782 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-12 21:27:11.517985 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-12 21:27:11.657434 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-12 21:27:11.80706 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-12 21:27:11.969699 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-12 21:27:12.129153 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-12 21:27:12.283194 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-12 21:27:12.445522 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-12 21:27:12.612348 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-12 21:27:12.764404 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-12 21:27:12.928496 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-12 21:27:13.08314 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-12 21:27:13.243667 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-12 21:27:13.405749 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-12 21:27:13.553518 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-12 21:27:13.703979 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-12 21:27:13.866489 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-12 21:27:14.023688 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-12 21:27:14.190671 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-12 21:27:14.363578 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-12 21:27:14.517746 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-12 21:27:14.672899 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-12 21:27:14.857461 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-12 21:27:15.030127 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-12 21:27:15.185289 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-12 21:27:15.345027 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-12 21:27:15.488181 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-12 21:27:15.649942 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-12 21:27:15.810414 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-12 21:27:15.961213 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-12 21:27:16.422663 INFO::Counting total values for each feature
2025-02-12 21:27:16.45512 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-12 21:27:16.579026 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-12 21:27:16.738948 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-12 21:27:16.889283 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-12 21:27:16.939821 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-12 21:27:16.96806 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-12 21:27:16.97466 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-12 21:27:16.981117 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"
2025-02-12 21:27:16.995699 INFO::Writing function arguments to log file
2025-02-12 21:27:17.004491 INFO::Verifying options selected are valid
2025-02-12 21:27:17.005558 INFO::Determining format of input files
2025-02-12 21:27:17.00697 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-12 21:27:17.01311 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-12 21:27:17.01556 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-12 21:27:17.018009 INFO::Filter data based on min abundance and min prevalence
2025-02-12 21:27:17.01898 INFO::Total samples in data: 1595
2025-02-12 21:27:17.019896 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-12 21:27:17.023623 INFO::Total filtered features: 0
2025-02-12 21:27:17.024727 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-12 21:27:17.034786 INFO::Total filtered features with variance filtering: 0
2025-02-12 21:27:17.036206 INFO::Filtered feature names from variance filtering:
2025-02-12 21:27:17.037437 INFO::Running selected normalization method: NONE
2025-02-12 21:27:17.038437 INFO::Bypass z-score application to metadata
2025-02-12 21:27:17.039462 INFO::Running selected transform method: AST
2025-02-12 21:27:17.056763 INFO::Running selected analysis method: LM
2025-02-12 21:27:17.058543 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-12 21:27:17.431293 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-12 21:27:17.577047 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-12 21:27:17.705291 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-12 21:27:17.870445 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-12 21:27:18.024729 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-12 21:27:18.167715 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-12 21:27:18.327697 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-12 21:27:18.486656 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-12 21:27:18.650786 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-12 21:27:18.80352 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-12 21:27:18.956845 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-12 21:27:19.116394 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-12 21:27:19.270037 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-12 21:27:19.424411 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-12 21:27:19.572726 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-12 21:27:19.737958 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-12 21:27:19.866109 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-12 21:27:20.001923 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-12 21:27:20.162912 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-12 21:27:20.333045 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-12 21:27:20.483407 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-12 21:27:20.633486 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-12 21:27:20.788376 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-12 21:27:20.948324 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-12 21:27:21.100347 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-12 21:27:21.251419 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-12 21:27:21.400909 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-12 21:27:21.576818 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-12 21:27:21.711011 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-12 21:27:21.851095 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-12 21:27:21.99869 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-12 21:27:22.153063 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-12 21:27:22.305343 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-12 21:27:22.462173 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-12 21:27:22.617654 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-12 21:27:22.779016 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-12 21:27:22.922311 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-12 21:27:23.077106 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-12 21:27:23.23093 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-12 21:27:23.379675 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-12 21:27:23.534258 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-12 21:27:23.686206 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-12 21:27:23.837105 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-12 21:27:24.005579 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-12 21:27:24.160858 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-12 21:27:24.30545 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-12 21:27:24.454801 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-12 21:27:24.618267 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-12 21:27:24.764235 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-12 21:27:24.915666 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-12 21:27:25.053239 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-12 21:27:25.224098 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-12 21:27:25.369545 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-12 21:27:25.51451 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-12 21:27:25.664771 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-12 21:27:25.823096 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-12 21:27:25.973277 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-12 21:27:26.124778 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-12 21:27:26.284927 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-12 21:27:26.476544 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-12 21:27:26.637688 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-12 21:27:26.788143 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-12 21:27:26.940782 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-12 21:27:27.109111 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-12 21:27:27.258748 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-12 21:27:27.421006 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-12 21:27:27.587242 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-12 21:27:27.701924 WARNING::Fitting problem for feature 67 a warning was issued
2025-02-12 21:27:27.864801 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-12 21:27:28.013478 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-12 21:27:28.191367 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-12 21:27:28.361262 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-12 21:27:28.521328 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-12 21:27:28.569893 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-12 21:27:28.725603 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-12 21:27:28.896159 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-12 21:27:29.051828 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-12 21:27:29.203696 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-12 21:27:29.346173 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-12 21:27:29.510876 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-12 21:27:29.658112 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-12 21:27:29.811183 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-12 21:27:29.952238 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-12 21:27:30.119158 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-12 21:27:30.281898 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-12 21:27:30.432373 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-12 21:27:30.577217 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-12 21:27:30.732064 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-12 21:27:30.887445 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-12 21:27:31.063478 INFO::Counting total values for each feature
2025-02-12 21:27:31.087263 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-12 21:27:31.230198 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-12 21:27:31.361858 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-12 21:27:31.521073 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-12 21:27:31.59905 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-12 21:27:31.671079 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-12 21:27:31.677953 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-12 21:27:31.684913 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 
 32.498   0.684  33.402

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	94.343	1.685	96.794