Multiple platform build/check report for BioC 3.20 - CHECK results for Maaslin2 on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
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*

CHECK results for Maaslin2 on palomino8

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: 1.20.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz

StartedAt: 2025-01-21 02:57:55 -0500 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 03:01:20 -0500 (Tue, 21 Jan 2025)

EllapsedTime: 204.9 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.20.0'
* 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 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 105.89   7.47  114.09
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 1.9.15
Current TMB package version is 1.9.16
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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 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"
2025-01-21 03:00:32.062924 INFO::Writing function arguments to log file
2025-01-21 03:00:32.132886 INFO::Verifying options selected are valid
2025-01-21 03:00:32.234924 INFO::Determining format of input files
2025-01-21 03:00:32.23822 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 03:00:32.250043 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 03:00:32.253453 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-21 03:00:32.258933 INFO::Filter data based on min abundance and min prevalence
2025-01-21 03:00:32.261169 INFO::Total samples in data: 1595
2025-01-21 03:00:32.270598 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 03:00:32.277954 INFO::Total filtered features: 0
2025-01-21 03:00:32.281169 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 03:00:32.293826 INFO::Total filtered features with variance filtering: 0
2025-01-21 03:00:32.295906 INFO::Filtered feature names from variance filtering:
2025-01-21 03:00:32.297656 INFO::Running selected normalization method: TSS
2025-01-21 03:00:33.68434 INFO::Bypass z-score application to metadata
2025-01-21 03:00:33.686371 INFO::Running selected transform method: AST
2025-01-21 03:00:33.705547 INFO::Running selected analysis method: LM
2025-01-21 03:00:34.315647 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 03:00:35.008116 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 03:00:35.24316 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 03:00:35.757488 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 03:00:35.938605 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 03:00:36.077346 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 03:00:36.217571 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 03:00:36.358107 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 03:00:36.488401 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 03:00:36.617204 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 03:00:36.768941 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 03:00:36.901844 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 03:00:37.038856 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 03:00:37.205314 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 03:00:37.468528 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 03:00:37.672349 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 03:00:37.879412 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 03:00:38.323855 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 03:00:38.483817 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 03:00:38.649552 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 03:00:38.855963 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 03:00:39.094405 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 03:00:39.290718 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 03:00:39.469558 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 03:00:39.627783 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 03:00:39.76089 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 03:00:39.932501 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 03:00:40.165393 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 03:00:40.339222 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 03:00:40.480643 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 03:00:40.627205 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 03:00:40.766658 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 03:00:40.901894 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 03:00:41.051032 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 03:00:41.197007 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 03:00:41.324184 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 03:00:41.472006 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 03:00:41.673603 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 03:00:41.846929 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 03:00:42.060662 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 03:00:42.267224 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 03:00:42.499265 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 03:00:42.727839 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 03:00:42.946064 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 03:00:43.149897 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 03:00:43.367873 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 03:00:43.58531 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 03:00:43.809116 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 03:00:44.047532 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 03:00:44.246906 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 03:00:44.430723 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 03:00:44.630322 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 03:00:44.764624 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 03:00:44.987278 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 03:00:45.189075 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 03:00:45.324144 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 03:00:45.527724 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 03:00:45.758837 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 03:00:45.928343 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 03:00:46.069629 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 03:00:46.20151 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 03:00:46.349561 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 03:00:46.479851 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 03:00:46.64034 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 03:00:46.780976 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 03:00:46.977239 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 03:00:47.160578 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 03:00:47.356703 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 03:00:47.543971 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 03:00:47.728065 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 03:00:47.988318 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 03:00:48.172803 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 03:00:48.389058 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 03:00:48.552198 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 03:00:48.683612 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 03:00:48.870163 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 03:00:49.082841 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 03:00:49.277439 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 03:00:49.472633 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 03:00:49.699517 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 03:00:49.897562 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 03:00:50.046507 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 03:00:50.259148 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 03:00:50.458653 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 03:00:50.587208 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 03:00:50.952805 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 03:00:51.081041 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 03:00:51.279327 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 03:00:51.580141 INFO::Counting total values for each feature
2025-01-21 03:00:51.631794 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-21 03:00:52.10628 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-21 03:00:52.604776 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-21 03:00:53.060685 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-21 03:00:53.104098 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-21 03:00:53.129877 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-21 03:00:53.136034 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-21 03:00:53.151347 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"
2025-01-21 03:00:53.222305 INFO::Writing function arguments to log file
2025-01-21 03:00:53.236819 INFO::Verifying options selected are valid
2025-01-21 03:00:53.23856 INFO::Determining format of input files
2025-01-21 03:00:53.240551 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 03:00:53.247712 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 03:00:53.249549 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-21 03:00:53.251991 INFO::Filter data based on min abundance and min prevalence
2025-01-21 03:00:53.254236 INFO::Total samples in data: 1595
2025-01-21 03:00:53.256661 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 03:00:53.262551 INFO::Total filtered features: 0
2025-01-21 03:00:53.264421 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 03:00:53.273815 INFO::Total filtered features with variance filtering: 0
2025-01-21 03:00:53.275757 INFO::Filtered feature names from variance filtering:
2025-01-21 03:00:53.2774 INFO::Running selected normalization method: NONE
2025-01-21 03:00:53.278937 INFO::Bypass z-score application to metadata
2025-01-21 03:00:53.28046 INFO::Running selected transform method: AST
2025-01-21 03:00:53.298898 INFO::Running selected analysis method: LM
2025-01-21 03:00:53.301388 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 03:00:53.458826 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 03:00:53.605322 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 03:00:53.728303 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 03:00:53.860802 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 03:00:54.054869 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 03:00:54.226386 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 03:00:54.415543 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 03:00:54.58737 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 03:00:54.779755 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-21 03:00:54.936375 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 03:00:55.119782 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 03:00:55.291706 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-21 03:00:55.4892 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 03:00:55.689898 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 03:00:55.875192 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 03:00:56.041955 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 03:00:56.223854 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 03:00:56.391264 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-21 03:00:56.600377 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 03:00:56.768242 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 03:00:56.956111 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 03:00:57.138035 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 03:00:57.287838 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 03:00:57.457887 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 03:00:57.608863 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 03:00:57.762076 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 03:00:57.90427 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 03:00:58.111617 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 03:00:58.333747 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 03:00:58.53929 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 03:00:58.736289 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 03:00:58.926555 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 03:00:59.12304 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 03:00:59.323413 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 03:00:59.542549 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 03:00:59.681155 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 03:00:59.852044 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 03:01:00.026353 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 03:01:00.193402 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 03:01:00.420922 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 03:01:00.616135 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 03:01:00.807552 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 03:01:00.948563 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 03:01:01.098452 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 03:01:01.225311 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 03:01:01.352468 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 03:01:01.489417 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 03:01:01.670188 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 03:01:01.810277 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 03:01:02.007782 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 03:01:02.179791 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 03:01:02.322614 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 03:01:02.507157 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 03:01:02.656428 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 03:01:02.841691 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 03:01:03.316085 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 03:01:03.515044 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 03:01:03.709438 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 03:01:03.92352 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 03:01:04.132374 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 03:01:04.3136 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 03:01:04.51237 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 03:01:04.701619 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 03:01:04.921456 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 03:01:05.069166 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 03:01:05.209548 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 03:01:05.362616 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 03:01:05.566429 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 03:01:05.730065 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 03:01:05.864577 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 03:01:06.036087 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 03:01:06.191807 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 03:01:06.373057 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 03:01:06.580829 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 03:01:06.654275 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-21 03:01:06.85568 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 03:01:07.068206 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 03:01:07.273297 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 03:01:07.474403 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 03:01:07.68528 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 03:01:07.871461 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 03:01:08.066091 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 03:01:08.274417 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 03:01:08.464574 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 03:01:08.676583 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 03:01:08.823575 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 03:01:08.979744 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 03:01:09.194244 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 03:01:09.388797 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 03:01:09.602856 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 03:01:09.847031 INFO::Counting total values for each feature
2025-01-21 03:01:09.888503 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-21 03:01:10.321118 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-21 03:01:10.609159 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-21 03:01:11.034902 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-21 03:01:11.113236 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-21 03:01:11.177084 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-21 03:01:11.185619 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-21 03:01:11.202836 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 
  38.93    1.23   41.65

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	105.89	7.47	114.09