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This page was generated on 2025-05-01 11:43 -0400 (Thu, 01 May 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4832
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4574
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson1macOS 13.6.6 Venturaarm644.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" 4553
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 1154/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.22.0  (landing page)
Lauren McIver
Snapshot Date: 2025-04-28 17:48 -0400 (Mon, 28 Apr 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_21
git_last_commit: fcec85e
git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025)
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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on kjohnson1

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: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2025-04-29 06:45:48 -0400 (Tue, 29 Apr 2025)
EndedAt: 2025-04-29 06:46:50 -0400 (Tue, 29 Apr 2025)
EllapsedTime: 61.6 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88129)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* 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 32.973  0.603  33.636
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

Maaslin2.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.22.0’
** 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 version 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-04-29 06:46:34.528856 INFO::Writing function arguments to log file
2025-04-29 06:46:34.544774 INFO::Verifying options selected are valid
2025-04-29 06:46:34.557848 INFO::Determining format of input files
2025-04-29 06:46:34.558526 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-29 06:46:34.560918 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-29 06:46:34.561488 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-29 06:46:34.562347 INFO::Filter data based on min abundance and min prevalence
2025-04-29 06:46:34.562658 INFO::Total samples in data: 1595
2025-04-29 06:46:34.562966 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-29 06:46:34.567254 INFO::Total filtered features: 0
2025-04-29 06:46:34.56782 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-29 06:46:34.571043 INFO::Total filtered features with variance filtering: 0
2025-04-29 06:46:34.571503 INFO::Filtered feature names from variance filtering:
2025-04-29 06:46:34.571793 INFO::Running selected normalization method: TSS
2025-04-29 06:46:34.976114 INFO::Bypass z-score application to metadata
2025-04-29 06:46:34.976744 INFO::Running selected transform method: AST
2025-04-29 06:46:34.983096 INFO::Running selected analysis method: LM
2025-04-29 06:46:35.209502 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-29 06:46:35.384786 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-29 06:46:35.44471 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-29 06:46:35.509679 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-29 06:46:35.568775 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-29 06:46:35.628865 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-29 06:46:35.689595 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-29 06:46:35.755919 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-29 06:46:35.815443 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-29 06:46:35.863392 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-29 06:46:35.930785 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-29 06:46:35.991273 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-29 06:46:36.052138 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-29 06:46:36.128582 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-29 06:46:36.189818 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-29 06:46:36.250982 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-29 06:46:36.314429 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-29 06:46:36.378829 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-29 06:46:36.445669 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-29 06:46:36.510189 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-29 06:46:36.571958 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-29 06:46:36.635075 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-29 06:46:36.700118 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-29 06:46:36.772154 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-29 06:46:36.829962 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-29 06:46:36.890766 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-29 06:46:36.953811 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-29 06:46:37.014954 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-29 06:46:37.077546 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-29 06:46:37.138077 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-29 06:46:37.204372 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-29 06:46:37.261575 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-29 06:46:37.323375 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-29 06:46:37.38797 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-29 06:46:37.450789 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-29 06:46:37.510443 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-29 06:46:37.575513 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-29 06:46:37.635828 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-29 06:46:37.700509 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-29 06:46:37.757731 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-29 06:46:37.816032 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-29 06:46:37.882026 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-29 06:46:37.941533 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-29 06:46:38.003997 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-29 06:46:38.067355 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-29 06:46:38.124922 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-29 06:46:38.189451 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-29 06:46:38.25171 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-29 06:46:38.31362 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-29 06:46:38.375158 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-29 06:46:38.433426 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-29 06:46:38.495373 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-29 06:46:38.553454 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-29 06:46:38.616463 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-29 06:46:38.679713 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-29 06:46:38.740591 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-29 06:46:38.801087 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-29 06:46:38.868544 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-29 06:46:38.925511 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-29 06:46:38.997146 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-29 06:46:39.056886 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-29 06:46:39.117711 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-29 06:46:39.182348 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-29 06:46:39.244041 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-29 06:46:39.30735 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-29 06:46:39.380156 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-29 06:46:39.436529 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-29 06:46:39.495149 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-29 06:46:39.550821 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-29 06:46:39.615254 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-29 06:46:39.677731 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-29 06:46:39.740072 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-29 06:46:39.803612 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-29 06:46:39.862726 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-29 06:46:39.921331 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-29 06:46:39.988497 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-29 06:46:40.049035 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-29 06:46:40.111647 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-29 06:46:40.176272 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-29 06:46:40.24201 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-29 06:46:40.307743 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-29 06:46:40.371506 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-29 06:46:40.434197 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-29 06:46:40.494614 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-29 06:46:40.556301 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-29 06:46:40.616135 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-29 06:46:40.679265 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-29 06:46:40.737428 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-29 06:46:40.816842 INFO::Counting total values for each feature
2025-04-29 06:46:40.830453 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-29 06:46:40.881787 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-29 06:46:40.942213 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-29 06:46:41.001867 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-29 06:46:41.030601 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-29 06:46:41.04624 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-29 06:46:41.049481 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-29 06:46:41.052417 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"
2025-04-29 06:46:41.058018 INFO::Writing function arguments to log file
2025-04-29 06:46:41.060255 INFO::Verifying options selected are valid
2025-04-29 06:46:41.060626 INFO::Determining format of input files
2025-04-29 06:46:41.061091 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-29 06:46:41.063329 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-29 06:46:41.063787 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-29 06:46:41.064394 INFO::Filter data based on min abundance and min prevalence
2025-04-29 06:46:41.064759 INFO::Total samples in data: 1595
2025-04-29 06:46:41.065066 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-29 06:46:41.066577 INFO::Total filtered features: 0
2025-04-29 06:46:41.067044 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-29 06:46:41.073929 INFO::Total filtered features with variance filtering: 0
2025-04-29 06:46:41.074596 INFO::Filtered feature names from variance filtering:
2025-04-29 06:46:41.074948 INFO::Running selected normalization method: NONE
2025-04-29 06:46:41.075239 INFO::Bypass z-score application to metadata
2025-04-29 06:46:41.075532 INFO::Running selected transform method: AST
2025-04-29 06:46:41.08131 INFO::Running selected analysis method: LM
2025-04-29 06:46:41.081964 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-29 06:46:41.141462 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-29 06:46:41.197748 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-29 06:46:41.254534 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-29 06:46:41.310755 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-29 06:46:41.37017 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-29 06:46:41.432035 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-29 06:46:41.488892 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-29 06:46:41.644387 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-29 06:46:41.701169 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-29 06:46:41.759685 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-29 06:46:41.811389 WARNING::Fitting problem for feature 11 a warning was issued
2025-04-29 06:46:41.87877 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-29 06:46:41.933241 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-29 06:46:41.98 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-29 06:46:42.039722 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-29 06:46:42.098691 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-29 06:46:42.155226 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-29 06:46:42.209331 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-29 06:46:42.271058 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-29 06:46:42.327746 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-29 06:46:42.383275 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-29 06:46:42.441094 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-29 06:46:42.501451 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-29 06:46:42.55774 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-29 06:46:42.611165 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-29 06:46:42.670979 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-29 06:46:42.72648 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-29 06:46:42.781157 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-29 06:46:42.838786 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-29 06:46:42.894835 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-29 06:46:42.947034 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-29 06:46:43.001356 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-29 06:46:43.059472 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-29 06:46:43.115749 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-29 06:46:43.169094 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-29 06:46:43.238818 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-29 06:46:43.295776 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-29 06:46:43.355733 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-29 06:46:43.418022 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-29 06:46:43.477566 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-29 06:46:43.529795 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-29 06:46:43.584038 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-29 06:46:43.643426 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-29 06:46:43.700505 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-29 06:46:43.759953 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-29 06:46:43.816787 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-29 06:46:43.876216 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-29 06:46:43.933225 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-29 06:46:43.987044 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-29 06:46:44.046916 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-29 06:46:44.101364 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-29 06:46:44.153562 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-29 06:46:44.213821 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-29 06:46:44.26649 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-29 06:46:44.31892 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-29 06:46:44.373721 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-29 06:46:44.432998 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-29 06:46:44.49102 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-29 06:46:44.544664 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-29 06:46:44.602975 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-29 06:46:44.659031 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-29 06:46:44.712148 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-29 06:46:44.769931 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-29 06:46:44.823593 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-29 06:46:44.880213 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-29 06:46:44.93841 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-29 06:46:44.994107 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-29 06:46:45.055076 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-29 06:46:45.111239 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-29 06:46:45.166178 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-29 06:46:45.229388 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-29 06:46:45.289951 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-29 06:46:45.348122 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-29 06:46:45.372971 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-29 06:46:45.429219 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-29 06:46:45.48673 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-29 06:46:45.54772 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-29 06:46:45.604333 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-29 06:46:45.666204 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-29 06:46:45.721633 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-29 06:46:45.78243 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-29 06:46:45.842401 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-29 06:46:45.906929 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-29 06:46:45.96933 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-29 06:46:46.028242 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-29 06:46:46.081876 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-29 06:46:46.140283 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-29 06:46:46.195854 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-29 06:46:46.257644 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-29 06:46:46.326332 INFO::Counting total values for each feature
2025-04-29 06:46:46.335654 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-29 06:46:46.386742 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-29 06:46:46.437685 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-29 06:46:46.505425 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-29 06:46:46.543804 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-29 06:46:46.580561 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-29 06:46:46.584079 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-29 06:46:46.586894 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 
 12.279   0.229  12.509

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin232.973 0.60333.636