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This page was generated on 2025-03-20 12:12 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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: 2025-03-17 13:00 -0400 (Mon, 17 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: 2025-03-18 09:00:37 -0000 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 09:03:57 -0000 (Tue, 18 Mar 2025)
EllapsedTime: 200.2 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 117.597  0.818 118.699
* 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"
2025-03-18 09:03:12.352359 INFO::Writing function arguments to log file
2025-03-18 09:03:12.405097 INFO::Verifying options selected are valid
2025-03-18 09:03:12.449718 INFO::Determining format of input files
2025-03-18 09:03:12.451623 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 09:03:12.458581 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 09:03:12.46052 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-18 09:03:12.464111 INFO::Filter data based on min abundance and min prevalence
2025-03-18 09:03:12.465559 INFO::Total samples in data: 1595
2025-03-18 09:03:12.466818 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 09:03:12.474849 INFO::Total filtered features: 0
2025-03-18 09:03:12.476516 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 09:03:12.503478 INFO::Total filtered features with variance filtering: 0
2025-03-18 09:03:12.505131 INFO::Filtered feature names from variance filtering:
2025-03-18 09:03:12.515094 INFO::Running selected normalization method: TSS
2025-03-18 09:03:13.882057 INFO::Bypass z-score application to metadata
2025-03-18 09:03:13.883693 INFO::Running selected transform method: AST
2025-03-18 09:03:13.902703 INFO::Running selected analysis method: LM
2025-03-18 09:03:14.494509 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 09:03:14.944222 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 09:03:15.175424 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 09:03:15.39512 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 09:03:15.620925 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 09:03:15.837252 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 09:03:16.050434 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 09:03:16.267308 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 09:03:16.47012 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 09:03:16.686413 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 09:03:16.902118 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 09:03:17.164871 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 09:03:17.377003 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 09:03:17.57209 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 09:03:17.79891 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 09:03:18.01523 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 09:03:18.226618 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 09:03:18.436919 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 09:03:18.652663 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 09:03:18.871568 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 09:03:19.073327 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 09:03:19.293397 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 09:03:19.511746 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 09:03:19.748481 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 09:03:19.967976 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 09:03:20.178821 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 09:03:20.392094 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 09:03:20.599248 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 09:03:20.819337 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 09:03:21.03188 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 09:03:21.276901 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 09:03:21.487226 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 09:03:21.71305 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 09:03:21.926977 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 09:03:22.196003 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 09:03:22.430483 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 09:03:22.659518 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 09:03:22.873933 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 09:03:23.102495 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 09:03:23.319052 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 09:03:23.538553 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 09:03:23.765159 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 09:03:23.998053 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 09:03:24.235752 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 09:03:24.442825 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 09:03:24.659182 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 09:03:24.887058 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 09:03:25.315372 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 09:03:25.535508 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 09:03:25.739515 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 09:03:25.958376 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 09:03:26.186519 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 09:03:26.402638 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 09:03:26.610846 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 09:03:27.019475 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 09:03:27.221148 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 09:03:27.439654 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 09:03:27.672554 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 09:03:27.870887 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 09:03:28.078083 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 09:03:28.300072 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 09:03:28.52341 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 09:03:28.735531 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 09:03:28.949631 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 09:03:29.178951 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 09:03:29.389551 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 09:03:29.608031 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 09:03:29.828584 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 09:03:30.019679 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 09:03:30.228379 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 09:03:30.454561 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 09:03:30.667395 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 09:03:30.877506 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 09:03:31.08107 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 09:03:31.280731 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 09:03:31.494187 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 09:03:31.708947 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 09:03:31.930538 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 09:03:32.156713 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 09:03:32.386123 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 09:03:32.620813 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 09:03:32.826385 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 09:03:33.051341 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 09:03:33.269432 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 09:03:33.467268 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 09:03:33.688978 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 09:03:33.890776 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 09:03:34.099256 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 09:03:34.360814 INFO::Counting total values for each feature
2025-03-18 09:03:34.416814 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-18 09:03:34.533044 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-18 09:03:34.651139 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-18 09:03:34.771151 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-18 09:03:34.827844 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-18 09:03:34.858739 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-18 09:03:34.865529 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-18 09:03:34.87263 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"
2025-03-18 09:03:34.891802 INFO::Writing function arguments to log file
2025-03-18 09:03:34.900847 INFO::Verifying options selected are valid
2025-03-18 09:03:34.902286 INFO::Determining format of input files
2025-03-18 09:03:34.903854 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 09:03:34.910589 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 09:03:34.912221 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-18 09:03:34.914537 INFO::Filter data based on min abundance and min prevalence
2025-03-18 09:03:34.915864 INFO::Total samples in data: 1595
2025-03-18 09:03:34.917128 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 09:03:34.9353 INFO::Total filtered features: 0
2025-03-18 09:03:34.936943 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 09:03:34.963305 INFO::Total filtered features with variance filtering: 0
2025-03-18 09:03:34.964802 INFO::Filtered feature names from variance filtering:
2025-03-18 09:03:34.966033 INFO::Running selected normalization method: NONE
2025-03-18 09:03:34.967236 INFO::Bypass z-score application to metadata
2025-03-18 09:03:34.968421 INFO::Running selected transform method: AST
2025-03-18 09:03:34.993996 INFO::Running selected analysis method: LM
2025-03-18 09:03:34.996049 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 09:03:35.198452 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 09:03:35.425148 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 09:03:35.618586 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 09:03:35.81977 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 09:03:36.025858 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 09:03:36.229488 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 09:03:36.432051 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 09:03:36.646306 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 09:03:36.811219 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-18 09:03:37.041785 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 09:03:37.269701 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 09:03:37.480096 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 09:03:37.683878 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 09:03:37.863016 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 09:03:38.081612 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 09:03:38.296469 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 09:03:38.501535 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 09:03:38.658864 WARNING::Fitting problem for feature 16 a warning was issued
2025-03-18 09:03:38.879904 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 09:03:39.095403 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 09:03:39.308358 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 09:03:39.517218 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 09:03:39.711617 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 09:03:39.911418 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 09:03:40.123161 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 09:03:40.310874 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 09:03:40.50969 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 09:03:40.719743 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 09:03:40.921448 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 09:03:41.124052 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 09:03:41.321953 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 09:03:41.513701 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 09:03:41.708016 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 09:03:41.932111 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 09:03:42.141675 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 09:03:42.363131 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 09:03:42.561854 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 09:03:42.76711 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 09:03:42.992868 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 09:03:43.204317 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 09:03:43.421103 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 09:03:43.606615 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 09:03:43.797923 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 09:03:44.006243 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 09:03:44.198813 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 09:03:44.412846 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 09:03:44.612539 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 09:03:44.821662 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 09:03:45.021986 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 09:03:45.225616 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 09:03:45.439581 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 09:03:45.886214 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 09:03:46.068528 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 09:03:46.270945 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 09:03:46.454857 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 09:03:46.653922 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 09:03:46.845876 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 09:03:47.048462 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 09:03:47.245167 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 09:03:47.457652 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 09:03:47.666382 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 09:03:47.88624 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 09:03:48.099917 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 09:03:48.328948 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 09:03:48.523814 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 09:03:48.722999 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 09:03:48.918216 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 09:03:49.121909 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 09:03:49.310285 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 09:03:49.505776 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 09:03:49.697422 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 09:03:49.912786 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 09:03:50.121767 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 09:03:50.323356 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 09:03:50.392518 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-18 09:03:50.601161 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 09:03:50.799321 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 09:03:50.997668 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 09:03:51.193403 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 09:03:51.409098 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 09:03:51.613592 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 09:03:51.823188 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 09:03:52.034147 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 09:03:52.251643 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 09:03:52.457723 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 09:03:52.651465 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 09:03:52.844563 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 09:03:53.059345 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 09:03:53.267276 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 09:03:53.485976 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 09:03:53.751737 INFO::Counting total values for each feature
2025-03-18 09:03:53.784943 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-18 09:03:53.90098 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-18 09:03:54.017972 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-18 09:03:54.13708 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-18 09:03:54.211559 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-18 09:03:54.282719 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-18 09:03:54.289271 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-18 09:03:54.294862 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 
 42.833   0.474  43.396

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2117.597 0.818118.699