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"	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 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: 2025-01-21 23:43:09 -0500 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 23:46:00 -0500 (Tue, 21 Jan 2025)

EllapsedTime: 170.6 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 92.364  1.736  94.326
* 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"
2025-01-21 23:45:16.61105 INFO::Writing function arguments to log file
2025-01-21 23:45:16.656875 INFO::Verifying options selected are valid
2025-01-21 23:45:16.680573 INFO::Determining format of input files
2025-01-21 23:45:16.681764 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 23:45:16.684954 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 23:45:16.686212 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-21 23:45:16.687674 INFO::Filter data based on min abundance and min prevalence
2025-01-21 23:45:16.68851 INFO::Total samples in data: 1595
2025-01-21 23:45:16.689594 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 23:45:16.693337 INFO::Total filtered features: 0
2025-01-21 23:45:16.69442 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 23:45:16.706344 INFO::Total filtered features with variance filtering: 0
2025-01-21 23:45:16.707301 INFO::Filtered feature names from variance filtering:
2025-01-21 23:45:16.707699 INFO::Running selected normalization method: TSS
2025-01-21 23:45:18.030884 INFO::Bypass z-score application to metadata
2025-01-21 23:45:18.032549 INFO::Running selected transform method: AST
2025-01-21 23:45:18.050813 INFO::Running selected analysis method: LM
2025-01-21 23:45:18.678802 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 23:45:19.107656 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 23:45:19.285343 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 23:45:19.465135 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 23:45:19.657312 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 23:45:19.834554 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 23:45:20.008631 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 23:45:20.212259 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 23:45:20.385761 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 23:45:20.55191 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 23:45:20.718915 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 23:45:20.902286 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 23:45:21.071849 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 23:45:21.218184 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 23:45:21.454523 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 23:45:21.632673 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 23:45:21.819422 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 23:45:21.991025 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 23:45:22.182445 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 23:45:22.357362 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 23:45:22.51846 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 23:45:22.984768 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 23:45:23.15698 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 23:45:23.337636 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 23:45:23.525195 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 23:45:23.707648 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 23:45:23.883879 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 23:45:24.057813 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 23:45:24.253021 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 23:45:24.420161 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 23:45:24.596338 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 23:45:24.770989 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 23:45:24.947983 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 23:45:25.11655 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 23:45:25.310106 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 23:45:25.4783 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 23:45:25.64898 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 23:45:25.833437 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 23:45:26.004797 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 23:45:26.166018 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 23:45:26.34043 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 23:45:26.515212 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 23:45:26.692848 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 23:45:26.881311 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 23:45:27.051109 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 23:45:27.21246 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 23:45:27.386925 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 23:45:27.56254 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 23:45:27.752698 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 23:45:27.917805 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 23:45:28.083182 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 23:45:28.259341 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 23:45:28.423015 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 23:45:28.601005 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 23:45:28.773371 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 23:45:28.941601 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 23:45:29.115637 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 23:45:29.302004 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 23:45:29.46057 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 23:45:29.639386 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 23:45:29.798219 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 23:45:29.980009 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 23:45:30.142031 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 23:45:30.319887 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 23:45:30.505181 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 23:45:30.666391 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 23:45:30.834332 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 23:45:31.009379 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 23:45:31.184638 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 23:45:31.351178 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 23:45:31.528617 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 23:45:31.714235 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 23:45:31.88046 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 23:45:32.048583 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 23:45:32.230724 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 23:45:32.40322 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 23:45:32.590082 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 23:45:32.764993 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 23:45:32.935948 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 23:45:33.408816 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 23:45:33.586494 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 23:45:33.757545 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 23:45:33.947731 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 23:45:34.140736 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 23:45:34.29993 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 23:45:34.469128 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 23:45:34.635459 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 23:45:34.816496 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 23:45:35.025228 INFO::Counting total values for each feature
2025-01-21 23:45:35.06524 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-21 23:45:35.212074 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-21 23:45:35.386106 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-21 23:45:35.559297 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-21 23:45:35.640096 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-21 23:45:35.684296 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-21 23:45:35.693582 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-21 23:45:35.702203 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 23:45:35.717753 INFO::Writing function arguments to log file
2025-01-21 23:45:35.72418 INFO::Verifying options selected are valid
2025-01-21 23:45:35.725269 INFO::Determining format of input files
2025-01-21 23:45:35.726521 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 23:45:35.732945 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 23:45:35.734205 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-21 23:45:35.735939 INFO::Filter data based on min abundance and min prevalence
2025-01-21 23:45:35.736832 INFO::Total samples in data: 1595
2025-01-21 23:45:35.73766 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 23:45:35.74245 INFO::Total filtered features: 0
2025-01-21 23:45:35.743645 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 23:45:35.752462 INFO::Total filtered features with variance filtering: 0
2025-01-21 23:45:35.753695 INFO::Filtered feature names from variance filtering:
2025-01-21 23:45:35.754545 INFO::Running selected normalization method: NONE
2025-01-21 23:45:35.75536 INFO::Bypass z-score application to metadata
2025-01-21 23:45:35.756155 INFO::Running selected transform method: AST
2025-01-21 23:45:35.787682 INFO::Running selected analysis method: LM
2025-01-21 23:45:35.789578 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 23:45:35.948572 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 23:45:36.110476 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 23:45:36.266674 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 23:45:36.443858 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 23:45:36.605522 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 23:45:36.778342 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 23:45:36.948945 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 23:45:37.119297 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 23:45:37.254427 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-21 23:45:37.436596 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 23:45:37.608845 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 23:45:37.790738 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 23:45:37.950396 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 23:45:38.088561 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 23:45:38.271644 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 23:45:38.434003 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 23:45:38.59997 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 23:45:38.757258 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 23:45:38.93543 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 23:45:39.100904 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 23:45:39.258526 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 23:45:39.449391 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 23:45:39.622752 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 23:45:39.789434 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 23:45:39.956943 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 23:45:40.125479 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 23:45:40.293351 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 23:45:40.46314 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 23:45:40.625696 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 23:45:40.781065 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 23:45:40.947744 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 23:45:41.107289 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 23:45:41.271832 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 23:45:41.453396 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 23:45:41.611846 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 23:45:41.775586 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 23:45:41.942113 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 23:45:42.1051 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 23:45:42.276258 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 23:45:42.439764 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 23:45:42.597384 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 23:45:42.772192 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 23:45:42.930457 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 23:45:43.093044 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 23:45:43.26151 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 23:45:43.443702 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 23:45:43.605437 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 23:45:43.774505 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 23:45:43.931181 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 23:45:44.113319 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 23:45:44.275083 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 23:45:44.416639 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 23:45:44.584853 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 23:45:44.735514 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 23:45:44.831939 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 23:45:44.919057 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 23:45:45.03936 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 23:45:45.15122 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 23:45:45.322247 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 23:45:45.485206 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 23:45:45.652873 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 23:45:45.749849 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 23:45:45.921782 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 23:45:46.083787 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 23:45:46.247899 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 23:45:46.409675 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 23:45:46.609252 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 23:45:46.768536 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 23:45:46.909332 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-21 23:45:47.100265 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 23:45:47.277121 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 23:45:47.443174 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 23:45:47.614807 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 23:45:47.773299 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 23:45:47.83261 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-21 23:45:48.007489 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 23:45:48.168121 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 23:45:48.341682 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 23:45:48.515308 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 23:45:48.693566 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 23:45:48.85086 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 23:45:49.014175 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 23:45:49.185656 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 23:45:49.359024 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 23:45:49.52889 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 23:45:49.685901 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 23:45:49.8422 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 23:45:50.018732 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 23:45:50.180116 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 23:45:50.352494 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 23:45:50.545136 INFO::Counting total values for each feature
2025-01-21 23:45:50.589785 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-21 23:45:50.735038 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-21 23:45:50.878943 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-21 23:45:51.04985 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-21 23:45:51.162998 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-21 23:45:51.266644 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-21 23:45:51.275851 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-21 23:45:51.282793 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 
 35.261   0.765  36.120

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	92.364	1.736	94.326