Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-26 11:47 -0400 (Wed, 26 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4783
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4552
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4581
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4533
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4463
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 1142/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-25 13:40 -0400 (Tue, 25 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on kjohnson3

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Maaslin2
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-03-25 19:56:27 -0400 (Tue, 25 Mar 2025)
EndedAt: 2025-03-25 19:57:26 -0400 (Tue, 25 Mar 2025)
EllapsedTime: 58.8 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) (2025-03-02 r87868)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 29.754  0.597  30.485
* 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 ‘1.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.16
Current TMB package version is 1.9.17
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
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"
2025-03-25 19:57:11.826948 INFO::Writing function arguments to log file
2025-03-25 19:57:11.843312 INFO::Verifying options selected are valid
2025-03-25 19:57:11.85606 INFO::Determining format of input files
2025-03-25 19:57:11.856677 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-25 19:57:11.859248 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-25 19:57:11.859781 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-25 19:57:11.860598 INFO::Filter data based on min abundance and min prevalence
2025-03-25 19:57:11.860898 INFO::Total samples in data: 1595
2025-03-25 19:57:11.86117 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-25 19:57:11.865597 INFO::Total filtered features: 0
2025-03-25 19:57:11.866044 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-25 19:57:11.869122 INFO::Total filtered features with variance filtering: 0
2025-03-25 19:57:11.869662 INFO::Filtered feature names from variance filtering:
2025-03-25 19:57:11.869983 INFO::Running selected normalization method: TSS
2025-03-25 19:57:12.304815 INFO::Bypass z-score application to metadata
2025-03-25 19:57:12.30549 INFO::Running selected transform method: AST
2025-03-25 19:57:12.311688 INFO::Running selected analysis method: LM
2025-03-25 19:57:12.51141 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-25 19:57:12.635625 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-25 19:57:12.695299 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-25 19:57:12.748105 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-25 19:57:12.805317 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-25 19:57:12.858408 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-25 19:57:12.913243 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-25 19:57:12.964419 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-25 19:57:13.020051 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-25 19:57:13.062035 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-25 19:57:13.137567 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-25 19:57:13.188059 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-25 19:57:13.240059 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-25 19:57:13.294207 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-25 19:57:13.347133 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-25 19:57:13.403304 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-25 19:57:13.45813 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-25 19:57:13.517083 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-25 19:57:13.570832 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-25 19:57:13.626565 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-25 19:57:13.67539 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-25 19:57:13.730716 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-25 19:57:13.782906 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-25 19:57:13.837332 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-25 19:57:13.890768 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-25 19:57:13.943361 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-25 19:57:13.999252 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-25 19:57:14.051675 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-25 19:57:14.105105 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-25 19:57:14.160802 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-25 19:57:14.217947 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-25 19:57:14.271238 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-25 19:57:14.325925 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-25 19:57:14.38148 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-25 19:57:14.439297 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-25 19:57:14.50012 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-25 19:57:14.551796 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-25 19:57:14.608136 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-25 19:57:14.661294 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-25 19:57:14.717459 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-25 19:57:14.770109 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-25 19:57:14.828252 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-25 19:57:14.879937 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-25 19:57:14.939735 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-25 19:57:14.990319 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-25 19:57:15.043543 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-25 19:57:15.098877 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-25 19:57:15.151338 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-25 19:57:15.306453 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-25 19:57:15.35825 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-25 19:57:15.412225 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-25 19:57:15.472214 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-25 19:57:15.524278 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-25 19:57:15.580874 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-25 19:57:15.646065 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-25 19:57:15.697647 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-25 19:57:15.751092 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-25 19:57:15.811992 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-25 19:57:15.862416 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-25 19:57:15.918592 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-25 19:57:15.975482 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-25 19:57:16.027588 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-25 19:57:16.082254 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-25 19:57:16.143335 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-25 19:57:16.197132 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-25 19:57:16.249024 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-25 19:57:16.304724 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-25 19:57:16.359063 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-25 19:57:16.417804 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-25 19:57:16.471583 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-25 19:57:16.530495 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-25 19:57:16.590132 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-25 19:57:16.642155 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-25 19:57:16.701038 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-25 19:57:16.753331 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-25 19:57:16.807802 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-25 19:57:16.867801 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-25 19:57:16.925083 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-25 19:57:16.981557 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-25 19:57:17.038608 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-25 19:57:17.096764 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-25 19:57:17.149703 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-25 19:57:17.211845 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-25 19:57:17.266659 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-25 19:57:17.319159 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-25 19:57:17.371629 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-25 19:57:17.427315 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-25 19:57:17.482955 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-25 19:57:17.549433 INFO::Counting total values for each feature
2025-03-25 19:57:17.565148 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-25 19:57:17.612544 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-25 19:57:17.66841 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-25 19:57:17.725369 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-25 19:57:17.753047 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-25 19:57:17.776301 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-25 19:57:17.779314 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-25 19:57:17.782097 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"
2025-03-25 19:57:17.786991 INFO::Writing function arguments to log file
2025-03-25 19:57:17.788905 INFO::Verifying options selected are valid
2025-03-25 19:57:17.789208 INFO::Determining format of input files
2025-03-25 19:57:17.789607 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-25 19:57:17.794656 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-25 19:57:17.795173 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-25 19:57:17.795791 INFO::Filter data based on min abundance and min prevalence
2025-03-25 19:57:17.796111 INFO::Total samples in data: 1595
2025-03-25 19:57:17.796399 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-25 19:57:17.798028 INFO::Total filtered features: 0
2025-03-25 19:57:17.798374 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-25 19:57:17.801473 INFO::Total filtered features with variance filtering: 0
2025-03-25 19:57:17.80183 INFO::Filtered feature names from variance filtering:
2025-03-25 19:57:17.802097 INFO::Running selected normalization method: NONE
2025-03-25 19:57:17.802361 INFO::Bypass z-score application to metadata
2025-03-25 19:57:17.802611 INFO::Running selected transform method: AST
2025-03-25 19:57:17.821034 INFO::Running selected analysis method: LM
2025-03-25 19:57:17.822059 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-25 19:57:17.875226 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-25 19:57:17.926869 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-25 19:57:17.981127 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-25 19:57:18.034035 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-25 19:57:18.092813 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-25 19:57:18.152346 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-25 19:57:18.209585 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-25 19:57:18.258313 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-25 19:57:18.308938 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-25 19:57:18.368652 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-25 19:57:18.419217 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-25 19:57:18.477381 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-25 19:57:18.53152 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-25 19:57:18.573796 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-25 19:57:18.628553 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-25 19:57:18.683503 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-25 19:57:18.734839 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-25 19:57:18.786275 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-25 19:57:18.843707 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-25 19:57:18.894652 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-25 19:57:18.949215 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-25 19:57:19.003029 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-25 19:57:19.059064 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-25 19:57:19.117872 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-25 19:57:19.16763 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-25 19:57:19.22319 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-25 19:57:19.272827 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-25 19:57:19.327033 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-25 19:57:19.378835 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-25 19:57:19.431398 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-25 19:57:19.480537 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-25 19:57:19.534815 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-25 19:57:19.584375 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-25 19:57:19.641327 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-25 19:57:19.69126 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-25 19:57:19.748364 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-25 19:57:19.80147 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-25 19:57:19.859031 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-25 19:57:19.916499 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-25 19:57:19.969876 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-25 19:57:20.033643 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-25 19:57:20.08324 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-25 19:57:20.146607 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-25 19:57:20.195264 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-25 19:57:20.246487 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-25 19:57:20.303651 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-25 19:57:20.353846 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-25 19:57:20.406974 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-25 19:57:20.461276 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-25 19:57:20.51336 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-25 19:57:20.571067 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-25 19:57:20.617637 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-25 19:57:20.669691 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-25 19:57:20.720353 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-25 19:57:20.765535 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-25 19:57:20.819223 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-25 19:57:20.870849 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-25 19:57:20.929007 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-25 19:57:20.978665 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-25 19:57:21.02934 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-25 19:57:21.087206 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-25 19:57:21.136649 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-25 19:57:21.192729 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-25 19:57:21.242274 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-25 19:57:21.292594 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-25 19:57:21.347819 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-25 19:57:21.397476 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-25 19:57:21.454012 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-25 19:57:21.505015 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-25 19:57:21.561398 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-25 19:57:21.61445 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-25 19:57:21.669913 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-25 19:57:21.724328 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-25 19:57:21.742082 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-25 19:57:21.800798 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-25 19:57:21.850543 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-25 19:57:21.906086 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-25 19:57:21.957043 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-25 19:57:22.014167 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-25 19:57:22.064222 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-25 19:57:22.119242 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-25 19:57:22.176835 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-25 19:57:22.227202 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-25 19:57:22.292819 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-25 19:57:22.342217 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-25 19:57:22.397584 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-25 19:57:22.446318 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-25 19:57:22.498296 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-25 19:57:22.56015 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-25 19:57:22.619838 INFO::Counting total values for each feature
2025-03-25 19:57:22.633612 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-25 19:57:22.681323 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-25 19:57:22.757349 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-25 19:57:22.814662 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-25 19:57:22.851158 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-25 19:57:22.885839 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-25 19:57:22.888936 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-25 19:57:22.891218 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 
 11.172   0.267  11.498

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin229.754 0.59730.485