Multiple platform build/check report for BioC 3.20 - CHECK results for Maaslin2 on kjohnson1

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 kjohnson1

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: /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_1.20.0.tar.gz

StartedAt: 2025-02-05 00:20:09 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 00:22:59 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 170.7 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 91.979  1.822  94.077
* 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-3.20-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-arm64/Resources/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) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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"
2025-02-05 00:22:16.950208 INFO::Writing function arguments to log file
2025-02-05 00:22:16.999977 INFO::Verifying options selected are valid
2025-02-05 00:22:17.043371 INFO::Determining format of input files
2025-02-05 00:22:17.04537 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 00:22:17.05222 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-05 00:22:17.053985 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-05 00:22:17.057137 INFO::Filter data based on min abundance and min prevalence
2025-02-05 00:22:17.058413 INFO::Total samples in data: 1595
2025-02-05 00:22:17.059303 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-05 00:22:17.064483 INFO::Total filtered features: 0
2025-02-05 00:22:17.065693 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 00:22:17.08328 INFO::Total filtered features with variance filtering: 0
2025-02-05 00:22:17.084817 INFO::Filtered feature names from variance filtering:
2025-02-05 00:22:17.08573 INFO::Running selected normalization method: TSS
2025-02-05 00:22:18.439518 INFO::Bypass z-score application to metadata
2025-02-05 00:22:18.4413 INFO::Running selected transform method: AST
2025-02-05 00:22:18.459696 INFO::Running selected analysis method: LM
2025-02-05 00:22:19.126516 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-05 00:22:19.570284 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-05 00:22:19.766391 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-05 00:22:19.9587 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-05 00:22:20.166485 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-05 00:22:20.352995 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-05 00:22:20.505988 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-05 00:22:20.613619 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-05 00:22:20.693791 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-05 00:22:20.762985 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-05 00:22:20.876743 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-05 00:22:21.018718 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-05 00:22:21.185744 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-05 00:22:21.363082 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-05 00:22:21.533044 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-05 00:22:21.691679 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-05 00:22:21.862749 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-05 00:22:22.043246 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-05 00:22:22.241432 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-05 00:22:22.402998 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-05 00:22:22.573278 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-05 00:22:22.794068 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-05 00:22:22.973636 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-05 00:22:23.150328 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-05 00:22:23.347416 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-05 00:22:23.521472 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-05 00:22:23.693249 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-05 00:22:23.869283 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-05 00:22:24.053695 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-05 00:22:24.231008 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-05 00:22:24.400014 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-05 00:22:24.590491 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-05 00:22:24.757641 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-05 00:22:24.935508 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-05 00:22:25.114395 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-05 00:22:25.285403 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-05 00:22:25.461588 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-05 00:22:25.649555 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-05 00:22:25.812913 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-05 00:22:25.986068 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-05 00:22:26.168827 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-05 00:22:26.336654 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-05 00:22:26.51455 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-05 00:22:26.690941 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-05 00:22:26.854889 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-05 00:22:27.028708 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-05 00:22:27.224122 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-05 00:22:27.406932 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-05 00:22:27.58506 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-05 00:22:27.75656 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-05 00:22:27.922731 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-05 00:22:28.102652 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-05 00:22:28.272636 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-05 00:22:28.460133 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-05 00:22:28.61945 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-05 00:22:28.801532 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-05 00:22:28.982172 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-05 00:22:29.142504 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-05 00:22:29.329247 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-05 00:22:29.50192 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-05 00:22:29.672835 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-05 00:22:29.839154 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-05 00:22:30.021356 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-05 00:22:30.193626 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-05 00:22:30.37068 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-05 00:22:30.542532 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-05 00:22:30.723149 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-05 00:22:30.892115 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-05 00:22:31.065392 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-05 00:22:31.257558 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-05 00:22:31.433055 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-05 00:22:31.888107 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-05 00:22:32.049915 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-05 00:22:32.22083 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-05 00:22:32.392657 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-05 00:22:32.558899 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-05 00:22:32.728997 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-05 00:22:32.913387 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-05 00:22:33.09565 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-05 00:22:33.27342 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-05 00:22:33.45989 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-05 00:22:33.634312 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-05 00:22:33.82397 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-05 00:22:33.993529 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-05 00:22:34.161928 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-05 00:22:34.311492 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-05 00:22:34.464984 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-05 00:22:34.568969 INFO::Counting total values for each feature
2025-02-05 00:22:34.593767 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-05 00:22:34.654817 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-05 00:22:34.751027 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-05 00:22:34.818138 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-05 00:22:34.875324 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-05 00:22:34.903809 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-05 00:22:34.913241 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-05 00:22:34.91782 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"
2025-02-05 00:22:34.926967 INFO::Writing function arguments to log file
2025-02-05 00:22:34.930369 INFO::Verifying options selected are valid
2025-02-05 00:22:34.930915 INFO::Determining format of input files
2025-02-05 00:22:34.931449 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 00:22:34.934196 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-05 00:22:34.934796 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-05 00:22:34.935528 INFO::Filter data based on min abundance and min prevalence
2025-02-05 00:22:34.935889 INFO::Total samples in data: 1595
2025-02-05 00:22:34.936195 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-05 00:22:34.938505 INFO::Total filtered features: 0
2025-02-05 00:22:34.939147 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 00:22:34.942984 INFO::Total filtered features with variance filtering: 0
2025-02-05 00:22:34.943812 INFO::Filtered feature names from variance filtering:
2025-02-05 00:22:34.944174 INFO::Running selected normalization method: NONE
2025-02-05 00:22:34.944501 INFO::Bypass z-score application to metadata
2025-02-05 00:22:34.944825 INFO::Running selected transform method: AST
2025-02-05 00:22:34.957282 INFO::Running selected analysis method: LM
2025-02-05 00:22:34.958305 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-05 00:22:35.077393 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-05 00:22:35.237996 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-05 00:22:35.388713 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-05 00:22:35.595592 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-05 00:22:35.766634 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-05 00:22:35.945558 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-05 00:22:36.124255 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-05 00:22:36.289612 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-05 00:22:36.460389 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-05 00:22:36.640764 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-05 00:22:36.811005 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-05 00:22:36.974222 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-05 00:22:37.153073 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-05 00:22:37.322391 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-05 00:22:37.495908 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-05 00:22:37.67665 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-05 00:22:37.853981 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-05 00:22:38.03912 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-05 00:22:38.196721 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-05 00:22:38.376866 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-05 00:22:38.571505 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-05 00:22:38.740244 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-05 00:22:38.91081 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-05 00:22:39.078989 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-05 00:22:39.246396 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-05 00:22:39.425685 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-05 00:22:39.596991 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-05 00:22:39.779044 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-05 00:22:39.93034 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-05 00:22:40.092101 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-05 00:22:40.263734 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-05 00:22:40.435813 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-05 00:22:40.608525 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-05 00:22:40.770161 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-05 00:22:40.943317 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-05 00:22:41.110797 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-05 00:22:41.2983 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-05 00:22:41.46776 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-05 00:22:41.62165 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-05 00:22:41.792016 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-05 00:22:41.950264 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-05 00:22:42.111615 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-05 00:22:42.291523 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-05 00:22:42.456558 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-05 00:22:42.636427 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-05 00:22:42.802148 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-05 00:22:42.954393 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-05 00:22:43.127317 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-05 00:22:43.28363 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-05 00:22:43.438883 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-05 00:22:43.619411 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-05 00:22:43.772607 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-05 00:22:43.949955 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-05 00:22:44.104901 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-05 00:22:44.275557 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-05 00:22:44.435717 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-05 00:22:44.596085 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-05 00:22:44.781019 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-05 00:22:44.944804 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-05 00:22:45.115123 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-05 00:22:45.272675 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-05 00:22:45.440184 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-05 00:22:45.604575 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-05 00:22:45.77855 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-05 00:22:45.950261 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-05 00:22:46.115536 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-05 00:22:46.292771 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-05 00:22:46.448522 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-05 00:22:46.628256 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-05 00:22:46.834512 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-05 00:22:46.998645 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-05 00:22:47.058015 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-05 00:22:47.234051 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-05 00:22:47.40967 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-05 00:22:47.569919 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-05 00:22:47.74649 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-05 00:22:47.910204 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-05 00:22:48.072244 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-05 00:22:48.248729 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-05 00:22:48.414829 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-05 00:22:48.587181 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-05 00:22:48.754292 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-05 00:22:48.927592 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-05 00:22:49.084938 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-05 00:22:49.244084 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-05 00:22:49.419465 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-05 00:22:49.589927 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-05 00:22:49.799419 INFO::Counting total values for each feature
2025-02-05 00:22:49.828557 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-05 00:22:49.97563 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-05 00:22:50.124413 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-05 00:22:50.296851 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-05 00:22:50.407614 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-05 00:22:50.513581 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-05 00:22:50.52309 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-05 00:22:50.530149 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 1 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 34.003   0.856  35.012

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	91.979	1.822	94.077