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This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-04-01 07:52:47 -0000 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 07:56:17 -0000 (Tue, 01 Apr 2025)
EllapsedTime: 210.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 loading without being on the library search path ... 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 119.747  1.085 121.173
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’
* installing *source* package ‘Maaslin2’ ...
** 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 version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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"
2025-04-01 07:55:33.252006 INFO::Writing function arguments to log file
2025-04-01 07:55:33.304621 INFO::Verifying options selected are valid
2025-04-01 07:55:33.348829 INFO::Determining format of input files
2025-04-01 07:55:33.350654 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 07:55:33.357214 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 07:55:33.359046 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-01 07:55:33.362459 INFO::Filter data based on min abundance and min prevalence
2025-04-01 07:55:33.363744 INFO::Total samples in data: 1595
2025-04-01 07:55:33.364972 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 07:55:33.372896 INFO::Total filtered features: 0
2025-04-01 07:55:33.374411 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 07:55:33.401514 INFO::Total filtered features with variance filtering: 0
2025-04-01 07:55:33.403038 INFO::Filtered feature names from variance filtering:
2025-04-01 07:55:33.412624 INFO::Running selected normalization method: TSS
2025-04-01 07:55:34.79057 INFO::Bypass z-score application to metadata
2025-04-01 07:55:34.792272 INFO::Running selected transform method: AST
2025-04-01 07:55:34.812193 INFO::Running selected analysis method: LM
2025-04-01 07:55:35.412873 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 07:55:35.869802 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 07:55:36.117471 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 07:55:36.332762 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 07:55:36.555951 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 07:55:36.770981 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 07:55:36.981452 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 07:55:37.200053 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 07:55:37.406465 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 07:55:37.619071 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 07:55:37.825594 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 07:55:38.097554 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 07:55:38.324871 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 07:55:38.530384 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-01 07:55:38.757477 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 07:55:38.975209 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 07:55:39.186712 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 07:55:39.399951 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 07:55:39.616009 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 07:55:39.841429 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 07:55:40.039729 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 07:55:40.262016 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 07:55:40.486769 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 07:55:40.708325 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 07:55:40.916136 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 07:55:41.127615 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 07:55:41.345729 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 07:55:41.555045 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 07:55:41.780041 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 07:55:41.989684 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 07:55:42.230299 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 07:55:42.438574 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 07:55:42.664511 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 07:55:42.878178 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 07:55:43.135488 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 07:55:43.350197 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 07:55:43.57154 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 07:55:43.785185 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 07:55:44.011721 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 07:55:44.215431 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 07:55:44.432917 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 07:55:44.650718 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 07:55:44.866313 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 07:55:45.091208 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 07:55:45.296534 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 07:55:45.50499 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 07:55:45.727535 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 07:55:46.161612 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 07:55:46.373857 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 07:55:46.581263 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 07:55:46.799526 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 07:55:47.01536 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 07:55:47.222483 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 07:55:47.440492 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 07:55:47.893679 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 07:55:48.095784 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 07:55:48.310126 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 07:55:48.547333 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 07:55:48.757095 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 07:55:48.965824 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 07:55:49.188701 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 07:55:49.410388 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 07:55:49.621186 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 07:55:49.844806 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 07:55:50.062797 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 07:55:50.262036 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 07:55:50.468009 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 07:55:50.681095 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 07:55:50.872117 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 07:55:51.083391 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 07:55:51.308134 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 07:55:51.525977 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 07:55:51.755582 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 07:55:51.958566 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 07:55:52.160042 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 07:55:52.371745 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 07:55:52.582467 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 07:55:52.810752 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 07:55:53.056619 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 07:55:53.280478 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 07:55:53.506126 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 07:55:53.711242 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 07:55:53.926578 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 07:55:54.147392 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 07:55:54.347022 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 07:55:54.57012 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 07:55:54.778811 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 07:55:54.996782 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 07:55:55.271218 INFO::Counting total values for each feature
2025-04-01 07:55:55.332014 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-01 07:55:55.449796 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-01 07:55:55.568153 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-01 07:55:55.689626 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-01 07:55:55.745719 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-01 07:55:55.776228 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-01 07:55:55.782769 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-01 07:55:55.789441 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"
2025-04-01 07:55:55.806689 INFO::Writing function arguments to log file
2025-04-01 07:55:55.814924 INFO::Verifying options selected are valid
2025-04-01 07:55:55.816399 INFO::Determining format of input files
2025-04-01 07:55:55.81798 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 07:55:55.825104 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 07:55:55.826775 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-01 07:55:55.829106 INFO::Filter data based on min abundance and min prevalence
2025-04-01 07:55:55.830333 INFO::Total samples in data: 1595
2025-04-01 07:55:55.831486 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 07:55:55.849671 INFO::Total filtered features: 0
2025-04-01 07:55:55.85128 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 07:55:55.877994 INFO::Total filtered features with variance filtering: 0
2025-04-01 07:55:55.879542 INFO::Filtered feature names from variance filtering:
2025-04-01 07:55:55.880787 INFO::Running selected normalization method: NONE
2025-04-01 07:55:55.881966 INFO::Bypass z-score application to metadata
2025-04-01 07:55:55.883121 INFO::Running selected transform method: AST
2025-04-01 07:55:55.911082 INFO::Running selected analysis method: LM
2025-04-01 07:55:55.913245 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 07:55:56.110735 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 07:55:56.329484 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 07:55:56.524638 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 07:55:56.732517 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 07:55:56.937896 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 07:55:57.142874 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 07:55:57.343248 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 07:55:57.558996 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 07:55:57.728477 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-01 07:55:57.966641 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 07:55:58.200237 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 07:55:58.402884 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 07:55:58.599164 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 07:55:58.774469 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-01 07:55:58.980157 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 07:55:59.18941 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 07:55:59.392514 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 07:55:59.555429 WARNING::Fitting problem for feature 16 a warning was issued
2025-04-01 07:55:59.78204 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 07:55:59.990785 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 07:56:00.192062 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 07:56:00.390487 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 07:56:00.585229 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 07:56:00.794976 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 07:56:01.017274 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 07:56:01.219925 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 07:56:01.429407 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 07:56:01.637167 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 07:56:01.831856 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 07:56:02.032175 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 07:56:02.23149 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 07:56:02.422534 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 07:56:02.620081 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 07:56:02.826518 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 07:56:03.052533 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 07:56:03.273696 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 07:56:03.473736 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 07:56:03.673875 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 07:56:03.884499 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 07:56:04.088095 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 07:56:04.312031 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 07:56:04.513809 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 07:56:04.714425 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 07:56:04.929354 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 07:56:05.125181 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 07:56:05.334283 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 07:56:05.527784 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 07:56:05.7299 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 07:56:05.929647 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 07:56:06.129979 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 07:56:06.32594 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 07:56:06.749119 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 07:56:06.932552 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 07:56:07.130681 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 07:56:07.315801 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 07:56:07.512571 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 07:56:07.703426 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 07:56:07.899811 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 07:56:08.099307 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 07:56:08.306141 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 07:56:08.508125 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 07:56:08.723315 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 07:56:08.925869 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 07:56:09.137791 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 07:56:09.332898 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 07:56:09.543126 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 07:56:09.750014 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 07:56:09.955328 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 07:56:10.148452 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 07:56:10.348839 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 07:56:10.540989 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 07:56:10.759258 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 07:56:10.972929 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 07:56:11.17579 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 07:56:11.245119 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-01 07:56:11.455443 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 07:56:11.649703 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 07:56:11.847044 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 07:56:12.045115 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 07:56:12.261297 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 07:56:12.454362 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 07:56:12.653159 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 07:56:12.860721 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 07:56:13.067057 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 07:56:13.280531 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 07:56:13.485138 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 07:56:13.686522 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 07:56:13.893043 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 07:56:14.087842 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 07:56:14.290035 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 07:56:14.535324 INFO::Counting total values for each feature
2025-04-01 07:56:14.567921 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-01 07:56:14.683646 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-01 07:56:14.799869 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-01 07:56:14.920827 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-01 07:56:14.996221 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-01 07:56:15.06725 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-01 07:56:15.073852 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-01 07:56:15.079484 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 42.679   0.462  43.242

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2119.747 1.085121.173