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This page was generated on 2025-05-01 11:42 -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 merida1

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 08:52:26 -0400 (Tue, 29 Apr 2025)
EndedAt: 2025-04-29 08:58:19 -0400 (Tue, 29 Apr 2025)
EllapsedTime: 353.4 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 r88126)
* 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 ‘1.22.0’
* 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 186.367  3.182 209.951
* 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 ‘1.22.0’
** 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 r88126) -- "How About a Twenty-Six"
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"
2025-04-29 08:57:00.061748 INFO::Writing function arguments to log file
2025-04-29 08:57:00.173846 INFO::Verifying options selected are valid
2025-04-29 08:57:00.316309 INFO::Determining format of input files
2025-04-29 08:57:00.319875 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-29 08:57:00.338006 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-29 08:57:00.349385 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-29 08:57:00.356226 INFO::Filter data based on min abundance and min prevalence
2025-04-29 08:57:00.358822 INFO::Total samples in data: 1595
2025-04-29 08:57:00.361186 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-29 08:57:00.382975 INFO::Total filtered features: 0
2025-04-29 08:57:00.385774 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-29 08:57:00.406134 INFO::Total filtered features with variance filtering: 0
2025-04-29 08:57:00.408888 INFO::Filtered feature names from variance filtering:
2025-04-29 08:57:00.412545 INFO::Running selected normalization method: TSS
2025-04-29 08:57:03.043947 INFO::Bypass z-score application to metadata
2025-04-29 08:57:03.046629 INFO::Running selected transform method: AST
2025-04-29 08:57:03.090058 INFO::Running selected analysis method: LM
2025-04-29 08:57:04.394057 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-29 08:57:05.698294 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-29 08:57:06.076555 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-29 08:57:06.465832 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-29 08:57:06.82674 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-29 08:57:07.182657 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-29 08:57:07.535517 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-29 08:57:07.898942 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-29 08:57:08.258609 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-29 08:57:08.601143 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-29 08:57:08.963844 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-29 08:57:09.319965 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-29 08:57:09.669257 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-29 08:57:10.00844 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-29 08:57:10.384885 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-29 08:57:10.737448 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-29 08:57:11.079705 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-29 08:57:11.432957 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-29 08:57:11.785524 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-29 08:57:12.13806 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-29 08:57:12.480516 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-29 08:57:12.822281 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-29 08:57:13.175447 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-29 08:57:13.537337 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-29 08:57:13.882985 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-29 08:57:14.241991 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-29 08:57:14.614164 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-29 08:57:14.972787 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-29 08:57:15.330051 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-29 08:57:15.686543 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-29 08:57:16.031758 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-29 08:57:16.35543 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-29 08:57:16.709658 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-29 08:57:17.047943 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-29 08:57:17.398615 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-29 08:57:17.728161 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-29 08:57:18.071162 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-29 08:57:18.430773 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-29 08:57:18.77794 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-29 08:57:19.094116 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-29 08:57:19.43685 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-29 08:57:19.781073 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-29 08:57:20.125179 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-29 08:57:20.467528 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-29 08:57:20.819172 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-29 08:57:21.168195 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-29 08:57:21.53732 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-29 08:57:21.878345 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-29 08:57:22.225009 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-29 08:57:22.562964 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-29 08:57:22.914772 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-29 08:57:23.258833 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-29 08:57:23.583598 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-29 08:57:23.930047 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-29 08:57:24.27578 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-29 08:57:24.590214 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-29 08:57:24.966776 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-29 08:57:25.336671 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-29 08:57:25.690086 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-29 08:57:26.078983 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-29 08:57:26.418472 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-29 08:57:26.743617 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-29 08:57:27.335921 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-29 08:57:27.685583 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-29 08:57:28.027123 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-29 08:57:28.364933 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-29 08:57:28.680522 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-29 08:57:28.987232 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-29 08:57:29.300536 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-29 08:57:29.617768 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-29 08:57:29.965642 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-29 08:57:30.324672 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-29 08:57:30.661804 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-29 08:57:30.997669 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-29 08:57:31.324482 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-29 08:57:31.661776 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-29 08:57:32.005306 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-29 08:57:32.338483 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-29 08:57:32.689564 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-29 08:57:33.033232 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-29 08:57:33.38649 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-29 08:57:33.735266 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-29 08:57:34.082736 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-29 08:57:34.423697 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-29 08:57:34.75748 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-29 08:57:35.09371 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-29 08:57:35.439899 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-29 08:57:35.769286 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-29 08:57:36.240481 INFO::Counting total values for each feature
2025-04-29 08:57:36.352542 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-29 08:57:36.635808 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-29 08:57:36.989858 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-29 08:57:37.342269 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-29 08:57:37.441248 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-29 08:57:37.494496 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-29 08:57:37.506017 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-29 08:57:37.521406 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 08:57:37.556024 INFO::Writing function arguments to log file
2025-04-29 08:57:37.571364 INFO::Verifying options selected are valid
2025-04-29 08:57:37.573821 INFO::Determining format of input files
2025-04-29 08:57:37.577662 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-29 08:57:37.591831 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-29 08:57:37.594668 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-29 08:57:37.599085 INFO::Filter data based on min abundance and min prevalence
2025-04-29 08:57:37.601466 INFO::Total samples in data: 1595
2025-04-29 08:57:37.603674 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-29 08:57:37.615683 INFO::Total filtered features: 0
2025-04-29 08:57:37.618569 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-29 08:57:37.63487 INFO::Total filtered features with variance filtering: 0
2025-04-29 08:57:37.647576 INFO::Filtered feature names from variance filtering:
2025-04-29 08:57:37.650379 INFO::Running selected normalization method: NONE
2025-04-29 08:57:37.653337 INFO::Bypass z-score application to metadata
2025-04-29 08:57:37.655632 INFO::Running selected transform method: AST
2025-04-29 08:57:37.683833 INFO::Running selected analysis method: LM
2025-04-29 08:57:37.68694 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-29 08:57:37.998082 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-29 08:57:38.324199 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-29 08:57:38.645707 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-29 08:57:38.987515 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-29 08:57:39.301043 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-29 08:57:39.622465 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-29 08:57:39.954557 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-29 08:57:40.271371 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-29 08:57:40.587796 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-29 08:57:40.912453 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-29 08:57:41.226244 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-29 08:57:41.540077 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-29 08:57:42.087955 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-29 08:57:42.443803 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-29 08:57:42.760761 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-29 08:57:43.078195 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-29 08:57:43.3923 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-29 08:57:43.706437 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-29 08:57:44.025316 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-29 08:57:44.332857 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-29 08:57:44.653763 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-29 08:57:44.967133 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-29 08:57:45.287911 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-29 08:57:45.587306 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-29 08:57:45.906012 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-29 08:57:46.234868 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-29 08:57:46.575544 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-29 08:57:46.885363 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-29 08:57:47.170804 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-29 08:57:47.467599 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-29 08:57:47.784153 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-29 08:57:48.096413 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-29 08:57:48.419625 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-29 08:57:49.005228 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-29 08:57:49.305702 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-29 08:57:49.613056 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-29 08:57:49.93175 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-29 08:57:50.267691 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-29 08:57:50.550391 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-29 08:57:50.847722 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-29 08:57:51.151234 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-29 08:57:51.472846 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-29 08:57:51.77912 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-29 08:57:52.097938 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-29 08:57:52.423178 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-29 08:57:52.725629 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-29 08:57:53.03761 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-29 08:57:53.337599 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-29 08:57:53.645196 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-29 08:57:53.950645 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-29 08:57:54.240163 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-29 08:57:54.560786 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-29 08:57:54.863158 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-29 08:57:55.169245 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-29 08:57:55.484954 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-29 08:57:55.809142 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-29 08:57:56.131186 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-29 08:57:56.448233 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-29 08:57:56.753538 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-29 08:57:57.071051 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-29 08:57:57.397642 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-29 08:57:57.687903 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-29 08:57:57.982128 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-29 08:57:58.310816 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-29 08:57:58.62382 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-29 08:57:58.943357 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-29 08:57:59.248237 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-29 08:57:59.505885 WARNING::Fitting problem for feature 67 a warning was issued
2025-04-29 08:57:59.878738 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-29 08:58:00.171649 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-29 08:58:00.491429 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-29 08:58:00.821789 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-29 08:58:01.130054 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-29 08:58:01.253787 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-29 08:58:01.586739 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-29 08:58:01.894542 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-29 08:58:02.223601 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-29 08:58:02.52891 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-29 08:58:02.853027 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-29 08:58:03.167537 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-29 08:58:03.493304 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-29 08:58:03.809926 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-29 08:58:04.131206 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-29 08:58:04.451765 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-29 08:58:04.773191 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-29 08:58:05.064824 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-29 08:58:05.387535 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-29 08:58:05.700676 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-29 08:58:06.028522 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-29 08:58:06.460161 INFO::Counting total values for each feature
2025-04-29 08:58:06.566871 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-29 08:58:06.939295 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-29 08:58:07.285304 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-29 08:58:07.702184 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-29 08:58:07.84544 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-29 08:58:07.986215 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-29 08:58:08.004412 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-29 08:58:08.018582 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 
 62.963   1.258  70.802

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2186.367 3.182209.951