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This page was generated on 2025-05-01 11:40 -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 palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.22.0.tar.gz
StartedAt: 2025-04-29 06:52:19 -0400 (Tue, 29 Apr 2025)
EndedAt: 2025-04-29 06:56:11 -0400 (Tue, 29 Apr 2025)
EllapsedTime: 231.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 113.78   6.89  134.62
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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

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

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-04-29 06:55:18.286754 INFO::Writing function arguments to log file
2025-04-29 06:55:18.543145 INFO::Verifying options selected are valid
2025-04-29 06:55:18.607195 INFO::Determining format of input files
2025-04-29 06:55:18.624427 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-29 06:55:18.682339 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-29 06:55:18.700269 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-29 06:55:18.719523 INFO::Filter data based on min abundance and min prevalence
2025-04-29 06:55:18.737055 INFO::Total samples in data: 1595
2025-04-29 06:55:18.758973 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-29 06:55:18.786624 INFO::Total filtered features: 0
2025-04-29 06:55:18.810005 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-29 06:55:18.841999 INFO::Total filtered features with variance filtering: 0
2025-04-29 06:55:18.864874 INFO::Filtered feature names from variance filtering:
2025-04-29 06:55:18.886869 INFO::Running selected normalization method: TSS
2025-04-29 06:55:20.103981 INFO::Bypass z-score application to metadata
2025-04-29 06:55:20.128229 INFO::Running selected transform method: AST
2025-04-29 06:55:20.174783 INFO::Running selected analysis method: LM
2025-04-29 06:55:20.816414 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-29 06:55:21.336504 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-29 06:55:21.598151 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-29 06:55:21.796161 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-29 06:55:21.979986 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-29 06:55:22.219566 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-29 06:55:22.603303 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-29 06:55:22.791796 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-29 06:55:22.935005 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-29 06:55:23.165842 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-29 06:55:23.392498 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-29 06:55:23.61645 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-29 06:55:23.793685 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-29 06:55:23.978263 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-29 06:55:24.174621 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-29 06:55:24.348268 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-29 06:55:24.568444 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-29 06:55:24.778026 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-29 06:55:24.986302 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-29 06:55:25.186015 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-29 06:55:25.390666 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-29 06:55:25.60219 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-29 06:55:25.796706 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-29 06:55:25.942456 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-29 06:55:26.127352 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-29 06:55:26.325608 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-29 06:55:26.501444 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-29 06:55:26.719109 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-29 06:55:26.93551 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-29 06:55:27.098129 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-29 06:55:27.330505 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-29 06:55:27.545598 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-29 06:55:27.725914 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-29 06:55:27.941866 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-29 06:55:28.09539 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-29 06:55:28.301376 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-29 06:55:28.539368 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-29 06:55:28.770821 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-29 06:55:29.006236 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-29 06:55:29.242107 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-29 06:55:29.469416 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-29 06:55:29.724265 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-29 06:55:29.938766 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-29 06:55:30.169031 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-29 06:55:30.599677 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-29 06:55:30.753916 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-29 06:55:30.897066 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-29 06:55:31.147997 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-29 06:55:31.382226 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-29 06:55:31.607886 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-29 06:55:31.754412 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-29 06:55:31.985185 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-29 06:55:32.190447 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-29 06:55:32.391298 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-29 06:55:32.627942 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-29 06:55:32.771619 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-29 06:55:32.987818 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-29 06:55:33.227234 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-29 06:55:33.427482 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-29 06:55:33.631595 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-29 06:55:33.841489 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-29 06:55:34.074292 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-29 06:55:34.289485 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-29 06:55:34.540613 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-29 06:55:34.767696 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-29 06:55:34.940287 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-29 06:55:35.106916 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-29 06:55:35.317607 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-29 06:55:35.531446 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-29 06:55:35.773927 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-29 06:55:36.0142 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-29 06:55:36.249792 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-29 06:55:36.435966 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-29 06:55:36.665819 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-29 06:55:36.905827 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-29 06:55:37.132637 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-29 06:55:37.330042 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-29 06:55:37.515759 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-29 06:55:37.694577 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-29 06:55:37.901088 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-29 06:55:38.132213 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-29 06:55:38.322726 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-29 06:55:38.530185 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-29 06:55:38.705824 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-29 06:55:38.910337 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-29 06:55:39.132325 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-29 06:55:39.354121 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-29 06:55:39.545456 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-29 06:55:39.807256 INFO::Counting total values for each feature
2025-04-29 06:55:39.879523 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-29 06:55:40.402483 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-29 06:55:40.805617 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-29 06:55:41.186279 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-29 06:55:41.263101 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-29 06:55:41.324648 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-29 06:55:41.373689 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-29 06:55:41.441351 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-04-29 06:55:41.51353 INFO::Writing function arguments to log file
2025-04-29 06:55:41.844023 INFO::Verifying options selected are valid
2025-04-29 06:55:41.859133 INFO::Determining format of input files
2025-04-29 06:55:41.874662 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-29 06:55:41.935724 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-29 06:55:41.956881 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-29 06:55:41.976709 INFO::Filter data based on min abundance and min prevalence
2025-04-29 06:55:42.011588 INFO::Total samples in data: 1595
2025-04-29 06:55:42.031984 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-29 06:55:42.053586 INFO::Total filtered features: 0
2025-04-29 06:55:42.071744 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-29 06:55:42.104811 INFO::Total filtered features with variance filtering: 0
2025-04-29 06:55:42.121743 INFO::Filtered feature names from variance filtering:
2025-04-29 06:55:42.142337 INFO::Running selected normalization method: NONE
2025-04-29 06:55:42.160474 INFO::Bypass z-score application to metadata
2025-04-29 06:55:42.178107 INFO::Running selected transform method: AST
2025-04-29 06:55:42.216942 INFO::Running selected analysis method: LM
2025-04-29 06:55:42.241583 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-29 06:55:42.430837 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-29 06:55:42.59718 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-29 06:55:42.740547 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-29 06:55:42.89427 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-29 06:55:43.102184 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-29 06:55:43.310804 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-29 06:55:43.799373 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-29 06:55:43.936875 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-29 06:55:44.118635 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-29 06:55:44.347655 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-29 06:55:44.584089 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-29 06:55:44.772584 WARNING::Fitting problem for feature 11 a warning was issued
2025-04-29 06:55:44.951944 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-29 06:55:45.16703 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-29 06:55:45.384467 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-29 06:55:45.580615 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-29 06:55:45.794122 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-29 06:55:45.932923 WARNING::Fitting problem for feature 16 a warning was issued
2025-04-29 06:55:46.183649 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-29 06:55:46.345579 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-29 06:55:46.536319 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-29 06:55:46.756889 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-29 06:55:46.977304 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-29 06:55:47.139392 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-29 06:55:47.376556 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-29 06:55:47.514956 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-29 06:55:47.713794 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-29 06:55:47.859334 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-29 06:55:48.011356 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-29 06:55:48.162204 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-29 06:55:48.350625 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-29 06:55:48.53575 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-29 06:55:48.744842 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-29 06:55:48.911849 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-29 06:55:49.092579 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-29 06:55:49.277045 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-29 06:55:49.484059 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-29 06:55:49.658 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-29 06:55:49.823944 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-29 06:55:49.971434 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-29 06:55:50.156783 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-29 06:55:50.29676 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-29 06:55:50.467273 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-29 06:55:50.668136 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-29 06:55:50.884107 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-29 06:55:51.062062 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-29 06:55:51.279159 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-29 06:55:51.43943 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-29 06:55:51.65464 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-29 06:55:51.822944 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-29 06:55:52.008018 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-29 06:55:52.218321 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-29 06:55:52.355112 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-29 06:55:52.576236 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-29 06:55:52.799061 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-29 06:55:52.984267 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-29 06:55:53.131693 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-29 06:55:53.329834 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-29 06:55:53.507216 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-29 06:55:53.658087 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-29 06:55:53.862005 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-29 06:55:54.089106 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-29 06:55:54.249649 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-29 06:55:54.425081 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-29 06:55:54.658263 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-29 06:55:54.867188 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-29 06:55:55.063868 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-29 06:55:55.239578 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-29 06:55:55.452781 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-29 06:55:55.639632 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-29 06:55:55.823948 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-29 06:55:55.971624 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-29 06:55:56.148454 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-29 06:55:56.35437 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-29 06:55:56.440651 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-29 06:55:56.658276 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-29 06:55:56.810762 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-29 06:55:56.988895 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-29 06:55:57.218806 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-29 06:55:57.436172 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-29 06:55:57.632037 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-29 06:55:57.833922 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-29 06:55:58.017246 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-29 06:55:58.262656 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-29 06:55:58.457279 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-29 06:55:58.678872 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-29 06:55:58.857761 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-29 06:55:59.087835 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-29 06:55:59.277554 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-29 06:55:59.500661 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-29 06:55:59.67774 INFO::Counting total values for each feature
2025-04-29 06:55:59.714534 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-29 06:56:00.143698 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-29 06:56:00.556466 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-29 06:56:01.031903 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-29 06:56:01.146635 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-29 06:56:01.484616 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-29 06:56:01.544052 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-29 06:56:01.610411 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 
  38.56    1.17   44.81

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2113.78 6.89134.62