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"	4753
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4501
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4524
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4476
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4407
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: 2025-02-04 03:16:57 -0500 (Tue, 04 Feb 2025)

EndedAt: 2025-02-04 03:20:27 -0500 (Tue, 04 Feb 2025)

EllapsedTime: 210.3 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 112.4   7.36   120.1
* 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"
2025-02-04 03:19:38.750808 INFO::Writing function arguments to log file
2025-02-04 03:19:38.800614 INFO::Verifying options selected are valid
2025-02-04 03:19:38.839543 INFO::Determining format of input files
2025-02-04 03:19:38.841832 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 03:19:38.852418 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-04 03:19:38.855611 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-04 03:19:38.860029 INFO::Filter data based on min abundance and min prevalence
2025-02-04 03:19:38.861737 INFO::Total samples in data: 1595
2025-02-04 03:19:38.870728 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-04 03:19:38.875936 INFO::Total filtered features: 0
2025-02-04 03:19:38.877959 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 03:19:38.888738 INFO::Total filtered features with variance filtering: 0
2025-02-04 03:19:38.890843 INFO::Filtered feature names from variance filtering:
2025-02-04 03:19:38.892985 INFO::Running selected normalization method: TSS
2025-02-04 03:19:40.532763 INFO::Bypass z-score application to metadata
2025-02-04 03:19:40.535893 INFO::Running selected transform method: AST
2025-02-04 03:19:40.566389 INFO::Running selected analysis method: LM
2025-02-04 03:19:41.030417 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-04 03:19:41.512527 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-04 03:19:41.664234 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-04 03:19:42.068425 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-04 03:19:42.283558 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-04 03:19:42.490239 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-04 03:19:42.705125 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-04 03:19:42.892083 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-04 03:19:43.105507 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-04 03:19:43.324745 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-04 03:19:43.554738 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-04 03:19:43.771536 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-04 03:19:43.944472 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-04 03:19:44.102473 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-04 03:19:44.330206 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-04 03:19:44.487535 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-04 03:19:44.670495 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-04 03:19:45.125452 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-04 03:19:45.294024 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-04 03:19:45.452578 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-04 03:19:45.631502 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-04 03:19:45.803275 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-04 03:19:45.950316 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-04 03:19:46.134438 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-04 03:19:46.303326 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-04 03:19:46.515576 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-04 03:19:46.678894 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-04 03:19:46.855744 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-04 03:19:47.075765 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-04 03:19:47.289408 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-04 03:19:47.523145 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-04 03:19:47.741279 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-04 03:19:47.963436 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-04 03:19:48.187431 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-04 03:19:48.399691 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-04 03:19:48.533878 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-04 03:19:48.681486 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-04 03:19:48.833433 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-04 03:19:48.983143 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-04 03:19:49.117646 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-04 03:19:49.289783 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-04 03:19:49.51333 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-04 03:19:49.743087 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-04 03:19:49.879811 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-04 03:19:50.037757 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-04 03:19:50.218207 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-04 03:19:50.427469 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-04 03:19:50.591966 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-04 03:19:50.743689 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-04 03:19:50.956713 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-04 03:19:51.188316 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-04 03:19:51.386643 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-04 03:19:51.584153 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-04 03:19:51.804435 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-04 03:19:51.990383 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-04 03:19:52.164939 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-04 03:19:52.295452 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-04 03:19:52.503484 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-04 03:19:52.709405 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-04 03:19:52.932722 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-04 03:19:53.075512 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-04 03:19:53.291008 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-04 03:19:53.503649 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-04 03:19:53.666899 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-04 03:19:53.805717 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-04 03:19:54.015667 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-04 03:19:54.218048 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-04 03:19:54.436797 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-04 03:19:54.650244 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-04 03:19:54.864956 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-04 03:19:55.143731 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-04 03:19:55.324038 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-04 03:19:55.499983 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-04 03:19:55.68412 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-04 03:19:55.827089 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-04 03:19:56.006697 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-04 03:19:56.233027 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-04 03:19:56.439143 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-04 03:19:56.642977 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-04 03:19:56.870373 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-04 03:19:57.051496 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-04 03:19:57.252701 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-04 03:19:57.440338 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-04 03:19:57.663866 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-04 03:19:57.826484 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-04 03:19:58.187239 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-04 03:19:58.315174 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-04 03:19:58.454277 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-04 03:19:58.710557 INFO::Counting total values for each feature
2025-02-04 03:19:58.765234 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-04 03:19:59.198328 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-04 03:19:59.627308 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-04 03:20:00.09479 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-04 03:20:00.158049 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-04 03:20:00.195804 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-04 03:20:00.205439 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-04 03:20:00.227524 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"
2025-02-04 03:20:00.279418 INFO::Writing function arguments to log file
2025-02-04 03:20:00.298904 INFO::Verifying options selected are valid
2025-02-04 03:20:00.301577 INFO::Determining format of input files
2025-02-04 03:20:00.304537 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 03:20:00.315635 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-04 03:20:00.318536 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-04 03:20:00.322287 INFO::Filter data based on min abundance and min prevalence
2025-02-04 03:20:00.324828 INFO::Total samples in data: 1595
2025-02-04 03:20:00.327306 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-04 03:20:00.335893 INFO::Total filtered features: 0
2025-02-04 03:20:00.33874 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 03:20:00.352664 INFO::Total filtered features with variance filtering: 0
2025-02-04 03:20:00.355614 INFO::Filtered feature names from variance filtering:
2025-02-04 03:20:00.358253 INFO::Running selected normalization method: NONE
2025-02-04 03:20:00.360869 INFO::Bypass z-score application to metadata
2025-02-04 03:20:00.363242 INFO::Running selected transform method: AST
2025-02-04 03:20:00.381682 INFO::Running selected analysis method: LM
2025-02-04 03:20:00.384211 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-04 03:20:00.554522 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-04 03:20:00.703602 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-04 03:20:00.900835 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-04 03:20:01.108654 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-04 03:20:01.349016 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-04 03:20:01.489505 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-04 03:20:01.701647 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-04 03:20:01.904801 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-04 03:20:02.044688 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-04 03:20:02.25088 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-04 03:20:02.391036 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-04 03:20:02.498392 WARNING::Fitting problem for feature 11 a warning was issued
2025-02-04 03:20:02.642702 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-04 03:20:02.825717 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-04 03:20:03.031763 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-04 03:20:03.235029 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-04 03:20:03.463525 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-04 03:20:03.629173 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-04 03:20:03.832564 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-04 03:20:04.02898 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-04 03:20:04.239642 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-04 03:20:04.412698 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-04 03:20:04.615047 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-04 03:20:04.757637 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-04 03:20:04.914694 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-04 03:20:05.068136 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-04 03:20:05.266725 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-04 03:20:05.437218 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-04 03:20:05.650837 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-04 03:20:05.815444 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-04 03:20:05.940846 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-04 03:20:06.084121 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-04 03:20:06.297482 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-04 03:20:06.453478 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-04 03:20:06.590878 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-04 03:20:06.726474 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-04 03:20:06.875441 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-04 03:20:07.03554 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-04 03:20:07.164379 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-04 03:20:07.583869 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-04 03:20:07.788462 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-04 03:20:07.956953 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-04 03:20:08.133978 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-04 03:20:08.366888 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-04 03:20:08.507313 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-04 03:20:08.664801 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-04 03:20:08.856861 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-04 03:20:09.019598 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-04 03:20:09.203323 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-04 03:20:09.33204 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-04 03:20:09.524852 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-04 03:20:09.729436 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-04 03:20:09.895536 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-04 03:20:10.055545 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-04 03:20:10.208801 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-04 03:20:10.413491 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-04 03:20:10.537256 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-04 03:20:10.662227 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-04 03:20:10.791774 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-04 03:20:10.968163 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-04 03:20:11.100919 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-04 03:20:11.234213 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-04 03:20:11.35779 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-04 03:20:11.708754 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-04 03:20:11.873121 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-04 03:20:11.998282 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-04 03:20:12.138841 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-04 03:20:12.308534 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-04 03:20:12.433012 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-04 03:20:12.639821 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-04 03:20:12.826642 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-04 03:20:12.967389 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-04 03:20:13.128157 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-04 03:20:13.324049 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-04 03:20:13.394602 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-04 03:20:13.613914 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-04 03:20:13.803388 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-04 03:20:13.94275 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-04 03:20:14.096404 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-04 03:20:14.325928 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-04 03:20:14.518486 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-04 03:20:14.683706 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-04 03:20:14.832517 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-04 03:20:15.004116 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-04 03:20:15.157614 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-04 03:20:15.286577 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-04 03:20:15.417469 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-04 03:20:15.647985 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-04 03:20:15.828172 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-04 03:20:16.02256 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-04 03:20:16.249039 INFO::Counting total values for each feature
2025-02-04 03:20:16.289432 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-04 03:20:16.71769 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-04 03:20:17.138082 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-04 03:20:17.562727 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-04 03:20:17.627317 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-04 03:20:17.685644 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-04 03:20:17.691853 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-04 03:20:17.703448 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 
  39.28    1.12   40.48

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	112.40	7.36	120.10