Multiple platform build/check report for BioC 3.20 - CHECK results for Maaslin2 on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4670
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4355
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4446
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4439
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4306
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: 1.20.0

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: 2025-03-07 05:45:54 -0500 (Fri, 07 Mar 2025)

EndedAt: 2025-03-07 05:51:30 -0500 (Fri, 07 Mar 2025)

EllapsedTime: 336.6 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 4.4.3 (2025-02-28)
* 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 12.7.6
* 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 179.781  2.745 195.171
* 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-x86_64/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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"
2025-03-07 05:50:11.715537 INFO::Writing function arguments to log file
2025-03-07 05:50:11.82408 INFO::Verifying options selected are valid
2025-03-07 05:50:11.915456 INFO::Determining format of input files
2025-03-07 05:50:11.92055 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-07 05:50:11.939755 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-07 05:50:11.949739 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-07 05:50:11.955754 INFO::Filter data based on min abundance and min prevalence
2025-03-07 05:50:11.959442 INFO::Total samples in data: 1595
2025-03-07 05:50:11.962134 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-07 05:50:11.973735 INFO::Total filtered features: 0
2025-03-07 05:50:11.976546 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-07 05:50:12.008387 INFO::Total filtered features with variance filtering: 0
2025-03-07 05:50:12.010943 INFO::Filtered feature names from variance filtering:
2025-03-07 05:50:12.014235 INFO::Running selected normalization method: TSS
2025-03-07 05:50:14.638318 INFO::Bypass z-score application to metadata
2025-03-07 05:50:14.640837 INFO::Running selected transform method: AST
2025-03-07 05:50:14.68139 INFO::Running selected analysis method: LM
2025-03-07 05:50:15.898573 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-07 05:50:16.703339 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-07 05:50:17.050183 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-07 05:50:17.392071 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-07 05:50:17.733853 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-07 05:50:18.054815 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-07 05:50:18.418011 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-07 05:50:18.752633 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-07 05:50:19.079353 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-07 05:50:19.390345 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-07 05:50:19.708367 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-07 05:50:20.038304 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-07 05:50:20.355366 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-07 05:50:20.631683 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-07 05:50:21.038729 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-07 05:50:21.368562 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-07 05:50:21.709418 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-07 05:50:22.046781 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-07 05:50:22.387819 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-07 05:50:22.715111 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-07 05:50:23.028715 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-07 05:50:23.359275 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-07 05:50:23.681287 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-07 05:50:24.042655 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-07 05:50:24.365082 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-07 05:50:24.692964 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-07 05:50:25.032585 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-07 05:50:25.694461 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-07 05:50:26.037636 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-07 05:50:26.379005 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-07 05:50:26.715134 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-07 05:50:27.035054 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-07 05:50:27.37799 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-07 05:50:27.733215 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-07 05:50:28.086831 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-07 05:50:28.433233 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-07 05:50:28.751867 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-07 05:50:29.334029 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-07 05:50:29.662549 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-07 05:50:29.973758 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-07 05:50:30.293859 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-07 05:50:30.631604 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-07 05:50:30.956222 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-07 05:50:31.290745 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-07 05:50:31.632217 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-07 05:50:31.943155 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-07 05:50:32.255385 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-07 05:50:32.586577 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-07 05:50:32.905168 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-07 05:50:33.21327 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-07 05:50:33.539786 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-07 05:50:33.841112 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-07 05:50:34.153201 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-07 05:50:34.521873 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-07 05:50:34.847504 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-07 05:50:35.150099 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-07 05:50:35.470848 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-07 05:50:35.796822 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-07 05:50:36.115441 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-07 05:50:36.429511 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-07 05:50:36.724229 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-07 05:50:37.043532 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-07 05:50:37.377743 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-07 05:50:37.751398 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-07 05:50:38.44852 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-07 05:50:38.761115 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-07 05:50:39.074468 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-07 05:50:39.388043 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-07 05:50:39.683389 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-07 05:50:40.01248 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-07 05:50:40.358489 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-07 05:50:40.675097 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-07 05:50:40.984292 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-07 05:50:41.305938 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-07 05:50:41.61291 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-07 05:50:41.922692 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-07 05:50:42.253703 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-07 05:50:42.621879 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-07 05:50:42.931834 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-07 05:50:43.288615 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-07 05:50:43.611688 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-07 05:50:43.931921 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-07 05:50:44.275925 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-07 05:50:44.595872 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-07 05:50:44.942495 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-07 05:50:45.24273 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-07 05:50:45.558611 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-07 05:50:45.902875 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-07 05:50:46.362751 INFO::Counting total values for each feature
2025-03-07 05:50:46.451738 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-07 05:50:46.751985 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-07 05:50:47.15805 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-07 05:50:47.550184 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-07 05:50:47.645823 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-07 05:50:47.697817 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-07 05:50:47.709196 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-07 05:50:47.727275 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"
2025-03-07 05:50:47.758077 INFO::Writing function arguments to log file
2025-03-07 05:50:47.776433 INFO::Verifying options selected are valid
2025-03-07 05:50:47.778935 INFO::Determining format of input files
2025-03-07 05:50:47.783441 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-07 05:50:47.795938 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-07 05:50:47.800455 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-07 05:50:47.804843 INFO::Filter data based on min abundance and min prevalence
2025-03-07 05:50:47.807363 INFO::Total samples in data: 1595
2025-03-07 05:50:47.809493 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-07 05:50:47.818198 INFO::Total filtered features: 0
2025-03-07 05:50:47.821893 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-07 05:50:47.837784 INFO::Total filtered features with variance filtering: 0
2025-03-07 05:50:47.84056 INFO::Filtered feature names from variance filtering:
2025-03-07 05:50:47.843125 INFO::Running selected normalization method: NONE
2025-03-07 05:50:47.845355 INFO::Bypass z-score application to metadata
2025-03-07 05:50:47.84756 INFO::Running selected transform method: AST
2025-03-07 05:50:47.882716 INFO::Running selected analysis method: LM
2025-03-07 05:50:47.886266 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-07 05:50:48.202414 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-07 05:50:48.526254 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-07 05:50:48.83938 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-07 05:50:49.149396 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-07 05:50:49.442384 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-07 05:50:49.757668 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-07 05:50:50.064734 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-07 05:50:50.361036 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-07 05:50:50.678299 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-07 05:50:50.990113 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-07 05:50:51.312663 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-07 05:50:51.610431 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-07 05:50:51.874641 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-07 05:50:52.209577 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-07 05:50:52.510527 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-07 05:50:52.82593 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-07 05:50:53.127719 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-07 05:50:53.441513 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-07 05:50:53.75283 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-07 05:50:54.047732 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-07 05:50:54.355435 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-07 05:50:54.936281 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-07 05:50:55.241059 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-07 05:50:55.573319 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-07 05:50:55.879256 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-07 05:50:56.203882 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-07 05:50:56.502252 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-07 05:50:56.80981 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-07 05:50:57.10835 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-07 05:50:57.411531 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-07 05:50:57.707544 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-07 05:50:57.996372 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-07 05:50:58.306234 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-07 05:50:58.585764 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-07 05:50:58.871216 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-07 05:50:59.162988 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-07 05:50:59.464413 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-07 05:50:59.750185 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-07 05:51:00.044389 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-07 05:51:00.338641 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-07 05:51:00.618978 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-07 05:51:00.904022 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-07 05:51:01.221715 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-07 05:51:01.547635 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-07 05:51:01.871586 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-07 05:51:02.21332 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-07 05:51:02.524574 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-07 05:51:02.823588 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-07 05:51:03.146349 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-07 05:51:03.455303 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-07 05:51:03.749073 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-07 05:51:04.059563 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-07 05:51:04.350185 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-07 05:51:04.636812 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-07 05:51:04.944656 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-07 05:51:05.236817 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-07 05:51:05.627476 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-07 05:51:05.939732 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-07 05:51:06.230844 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-07 05:51:06.558935 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-07 05:51:06.869082 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-07 05:51:07.205536 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-07 05:51:07.520461 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-07 05:51:07.827589 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-07 05:51:08.125189 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-07 05:51:08.413305 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-07 05:51:08.789577 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-07 05:51:09.074558 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-07 05:51:09.389144 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-07 05:51:09.669445 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-07 05:51:09.972166 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-07 05:51:10.330087 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-07 05:51:10.640627 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-07 05:51:10.758968 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-07 05:51:11.071466 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-07 05:51:11.360968 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-07 05:51:11.651615 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-07 05:51:11.988341 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-07 05:51:12.2833 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-07 05:51:12.567868 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-07 05:51:12.873358 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-07 05:51:13.175174 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-07 05:51:13.465918 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-07 05:51:13.772637 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-07 05:51:14.055797 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-07 05:51:14.348931 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-07 05:51:14.632507 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-07 05:51:14.940724 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-07 05:51:15.279097 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-07 05:51:15.681945 INFO::Counting total values for each feature
2025-03-07 05:51:15.761688 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-07 05:51:16.05086 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-07 05:51:16.357494 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-07 05:51:16.741269 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-07 05:51:16.860191 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-07 05:51:17.004273 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-07 05:51:17.016598 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-07 05:51:17.030478 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 
 62.679   1.099  68.179

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	179.781	2.745	195.171