Multiple platform build/check report for BioC 3.19 - CHECK results for Maaslin2 on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4747
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4489
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4518
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4467
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 merida1

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: 1.18.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.18.0.tar.gz

StartedAt: 2024-07-22 07:28:24 -0400 (Mon, 22 Jul 2024)

EndedAt: 2024-07-22 07:35:20 -0400 (Mon, 22 Jul 2024)

EllapsedTime: 416.4 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* 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 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 186.884  3.461 245.278
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.14
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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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"
2024-07-22 07:33:45.469406 INFO::Writing function arguments to log file
2024-07-22 07:33:45.600311 INFO::Verifying options selected are valid
2024-07-22 07:33:45.70557 INFO::Determining format of input files
2024-07-22 07:33:45.71326 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-22 07:33:45.732202 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-22 07:33:45.737967 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-22 07:33:45.744392 INFO::Filter data based on min abundance and min prevalence
2024-07-22 07:33:45.747006 INFO::Total samples in data: 1595
2024-07-22 07:33:45.751214 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-22 07:33:45.778743 INFO::Total filtered features: 0
2024-07-22 07:33:45.781742 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-22 07:33:45.807577 INFO::Total filtered features with variance filtering: 0
2024-07-22 07:33:45.815807 INFO::Filtered feature names from variance filtering:
2024-07-22 07:33:45.818877 INFO::Running selected normalization method: TSS
2024-07-22 07:33:48.891242 INFO::Bypass z-score application to metadata
2024-07-22 07:33:48.895054 INFO::Running selected transform method: AST
2024-07-22 07:33:48.945098 INFO::Running selected analysis method: LM
2024-07-22 07:33:50.383745 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-22 07:33:51.345799 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-22 07:33:51.78201 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-22 07:33:52.187161 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-22 07:33:52.614339 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-22 07:33:53.023583 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-22 07:33:53.431046 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-22 07:33:53.848517 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-22 07:33:54.259373 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-22 07:33:54.706095 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-22 07:33:55.107294 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-22 07:33:55.51955 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-22 07:33:55.917287 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-22 07:33:56.265814 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-22 07:33:56.698451 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-22 07:33:57.120451 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-22 07:33:57.533163 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-22 07:33:57.918291 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-22 07:33:58.36582 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-22 07:33:58.913069 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-22 07:33:59.440551 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-22 07:33:59.909887 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-22 07:34:00.361726 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-22 07:34:00.783337 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-22 07:34:01.179631 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-22 07:34:01.59752 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-22 07:34:02.011839 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-22 07:34:02.406192 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-22 07:34:02.822406 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-22 07:34:03.266066 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-22 07:34:03.67841 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-22 07:34:04.11244 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-22 07:34:04.512164 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-22 07:34:04.909971 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-22 07:34:05.325079 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-22 07:34:05.715474 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-22 07:34:06.12598 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-22 07:34:06.526932 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-22 07:34:06.953394 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-22 07:34:07.337056 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-22 07:34:07.744513 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-22 07:34:08.141632 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-22 07:34:08.561768 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-22 07:34:08.976965 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-22 07:34:09.367983 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-22 07:34:09.755322 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-22 07:34:10.163356 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-22 07:34:10.582584 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-22 07:34:11.324855 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-22 07:34:11.704494 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-22 07:34:12.089721 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-22 07:34:12.483619 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-22 07:34:12.861433 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-22 07:34:13.25816 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-22 07:34:13.676576 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-22 07:34:14.077122 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-22 07:34:14.468104 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-22 07:34:14.873231 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-22 07:34:15.276411 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-22 07:34:15.650464 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-22 07:34:16.056347 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-22 07:34:16.459062 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-22 07:34:16.86763 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-22 07:34:17.259718 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-22 07:34:17.655141 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-22 07:34:18.005718 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-22 07:34:18.38706 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-22 07:34:18.772579 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-22 07:34:19.152615 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-22 07:34:19.569051 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-22 07:34:20.010824 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-22 07:34:20.435477 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-22 07:34:20.817401 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-22 07:34:21.191369 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-22 07:34:21.560646 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-22 07:34:21.96575 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-22 07:34:22.364186 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-22 07:34:22.752193 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-22 07:34:23.148571 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-22 07:34:23.56641 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-22 07:34:24.070697 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-22 07:34:24.518401 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-22 07:34:24.969894 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-22 07:34:25.342502 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-22 07:34:25.72404 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-22 07:34:26.100754 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-22 07:34:26.52338 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-22 07:34:26.897192 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-22 07:34:27.448675 INFO::Counting total values for each feature
2024-07-22 07:34:27.577484 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-22 07:34:27.909668 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-22 07:34:28.337115 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-22 07:34:28.764065 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-22 07:34:28.883358 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-22 07:34:28.952102 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-22 07:34:28.966284 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-22 07:34:28.991279 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"
2024-07-22 07:34:29.030815 INFO::Writing function arguments to log file
2024-07-22 07:34:29.057947 INFO::Verifying options selected are valid
2024-07-22 07:34:29.061819 INFO::Determining format of input files
2024-07-22 07:34:29.06483 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-22 07:34:29.084402 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-22 07:34:29.086995 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-22 07:34:29.091231 INFO::Filter data based on min abundance and min prevalence
2024-07-22 07:34:29.096196 INFO::Total samples in data: 1595
2024-07-22 07:34:29.100425 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-22 07:34:29.113215 INFO::Total filtered features: 0
2024-07-22 07:34:29.116129 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-22 07:34:29.160009 INFO::Total filtered features with variance filtering: 0
2024-07-22 07:34:29.162641 INFO::Filtered feature names from variance filtering:
2024-07-22 07:34:29.165462 INFO::Running selected normalization method: NONE
2024-07-22 07:34:29.171616 INFO::Bypass z-score application to metadata
2024-07-22 07:34:29.173997 INFO::Running selected transform method: AST
2024-07-22 07:34:29.217947 INFO::Running selected analysis method: LM
2024-07-22 07:34:29.221381 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-22 07:34:29.64451 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-22 07:34:30.0446 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-22 07:34:30.417209 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-22 07:34:30.819332 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-22 07:34:31.177099 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-22 07:34:31.559776 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-22 07:34:31.93635 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-22 07:34:32.327888 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-22 07:34:32.692574 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-22 07:34:33.084655 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-22 07:34:33.461888 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-22 07:34:33.830725 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-22 07:34:34.151915 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-22 07:34:34.585011 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-22 07:34:34.96382 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-22 07:34:35.375058 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-22 07:34:35.740155 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-22 07:34:36.13021 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-22 07:34:36.531785 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-22 07:34:36.893503 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-22 07:34:37.282393 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-22 07:34:37.696171 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-22 07:34:38.056954 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-22 07:34:38.426558 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-22 07:34:38.860397 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-22 07:34:39.249087 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-22 07:34:39.640793 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-22 07:34:40.027121 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-22 07:34:40.427955 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-22 07:34:40.795907 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-22 07:34:41.16608 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-22 07:34:41.562767 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-22 07:34:41.944165 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-22 07:34:42.316374 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-22 07:34:42.690603 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-22 07:34:43.06131 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-22 07:34:43.447658 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-22 07:34:43.824295 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-22 07:34:44.203653 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-22 07:34:44.574836 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-22 07:34:44.925815 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-22 07:34:45.304125 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-22 07:34:45.687912 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-22 07:34:46.069944 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-22 07:34:46.775856 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-22 07:34:47.151347 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-22 07:34:47.527227 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-22 07:34:47.898761 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-22 07:34:48.306504 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-22 07:34:48.681475 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-22 07:34:49.05051 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-22 07:34:49.455656 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-22 07:34:49.809356 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-22 07:34:50.152374 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-22 07:34:50.523021 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-22 07:34:50.887391 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-22 07:34:51.263513 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-22 07:34:51.650454 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-22 07:34:52.040685 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-22 07:34:52.428362 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-22 07:34:52.78552 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-22 07:34:53.159065 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-22 07:34:53.523888 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-22 07:34:53.891651 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-22 07:34:54.261014 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-22 07:34:54.645614 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-22 07:34:55.032081 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-22 07:34:55.348521 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-22 07:34:55.758079 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-22 07:34:56.128403 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-22 07:34:56.526632 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-22 07:34:56.932076 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-22 07:34:57.327354 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-22 07:34:57.457502 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-22 07:34:57.829356 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-22 07:34:58.21323 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-22 07:34:58.583874 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-22 07:34:58.961031 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-22 07:34:59.361892 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-22 07:34:59.722225 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-22 07:35:00.098873 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-22 07:35:00.503592 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-22 07:35:00.872928 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-22 07:35:01.25005 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-22 07:35:01.618983 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-22 07:35:01.995424 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-22 07:35:02.358169 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-22 07:35:02.725402 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-22 07:35:03.124727 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-22 07:35:03.604836 INFO::Counting total values for each feature
2024-07-22 07:35:03.693502 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-22 07:35:04.025151 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-22 07:35:04.360882 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-22 07:35:04.846154 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-22 07:35:04.992017 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-22 07:35:05.538608 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-22 07:35:05.55063 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-22 07:35:05.571813 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 63.379   1.245  83.528

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	186.884	3.461	245.278