Sagun Maharjan
| Snapshot Date: 2026-05-18 13:45 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 6335054 |
| git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-19 12:54 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4898 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4617 |
| 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 | ||||
| Package 1183/2377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.27.0 (landing page) Sagun Maharjan
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| See other builds for Maaslin2 in R Universe. | ||||||||||||||
|
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. |
| Package: Maaslin2 |
| Version: 1.27.0 |
| 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_1.27.0.tar.gz |
| StartedAt: 2026-05-18 22:17:58 -0400 (Mon, 18 May 2026) |
| EndedAt: 2026-05-18 22:19:07 -0400 (Mon, 18 May 2026) |
| EllapsedTime: 69.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-19 02:17:58 UTC
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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: no visible binding for global variable ‘var’
maaslin2_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
var xnames
Consider adding
importFrom("stats", "var")
to your NAMESPACE file.
* 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 39.606 0.493 40.194
* 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-3.24-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.27.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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)
Maaslin2.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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"
2026-05-18 22:18:53.473896 INFO::Writing function arguments to log file
2026-05-18 22:18:53.484578 INFO::Verifying options selected are valid
2026-05-18 22:18:53.497904 INFO::Determining format of input files
2026-05-18 22:18:53.498609 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-18 22:18:53.500977 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-18 22:18:53.501521 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-18 22:18:53.505227 INFO::Filter data based on min abundance and min prevalence
2026-05-18 22:18:53.505718 INFO::Total samples in data: 1595
2026-05-18 22:18:53.506107 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-18 22:18:53.507683 INFO::Total filtered features: 0
2026-05-18 22:18:53.50814 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-18 22:18:53.511115 INFO::Total filtered features with variance filtering: 0
2026-05-18 22:18:53.511612 INFO::Filtered feature names from variance filtering:
2026-05-18 22:18:53.511992 INFO::Running selected normalization method: TSS
2026-05-18 22:18:53.897741 INFO::Bypass z-score application to metadata
2026-05-18 22:18:53.898485 INFO::Running selected transform method: AST
2026-05-18 22:18:53.908904 INFO::Running selected analysis method: LM
2026-05-18 22:18:54.17586 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-18 22:18:54.399592 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-18 22:18:54.460287 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-18 22:18:54.510794 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-18 22:18:54.563053 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-18 22:18:54.619354 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-18 22:18:54.670505 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-18 22:18:54.725507 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-18 22:18:54.781331 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-18 22:18:54.829746 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-18 22:18:54.880909 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-18 22:18:54.952159 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-18 22:18:55.001016 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-18 22:18:55.054027 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-18 22:18:55.104614 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-18 22:18:55.160431 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-18 22:18:55.208384 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-18 22:18:55.261444 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-18 22:18:55.316125 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-18 22:18:55.363118 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-18 22:18:55.411136 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-18 22:18:55.466552 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-18 22:18:55.519705 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-18 22:18:55.570826 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-18 22:18:55.627134 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-18 22:18:55.683619 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-18 22:18:55.73414 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-18 22:18:55.79314 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-18 22:18:55.846857 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-18 22:18:55.900335 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-18 22:18:55.954705 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-18 22:18:56.008759 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-18 22:18:56.059142 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-18 22:18:56.115902 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-18 22:18:56.16344 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-18 22:18:56.217948 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-18 22:18:56.2675 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-18 22:18:56.319345 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-18 22:18:56.372891 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-18 22:18:56.426066 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-18 22:18:56.488451 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-18 22:18:56.541554 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-18 22:18:56.5964 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-18 22:18:56.655811 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-18 22:18:56.710266 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-18 22:18:56.761808 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-18 22:18:56.818843 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-18 22:18:56.875281 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-18 22:18:56.928241 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-18 22:18:56.986671 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-18 22:18:57.039389 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-18 22:18:57.096247 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-18 22:18:57.152306 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-18 22:18:57.207496 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-18 22:18:57.25825 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-18 22:18:57.318171 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-18 22:18:57.375434 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-18 22:18:57.430082 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-18 22:18:57.48463 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-18 22:18:57.535455 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-18 22:18:57.590362 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-18 22:18:57.64507 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-18 22:18:57.704346 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-18 22:18:57.758211 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-18 22:18:57.808762 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-18 22:18:57.863717 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-18 22:18:57.915888 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-18 22:18:57.967719 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-18 22:18:58.021547 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-18 22:18:58.083773 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-18 22:18:58.141882 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-18 22:18:58.306164 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-18 22:18:58.356432 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-18 22:18:58.404322 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-18 22:18:58.45582 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-18 22:18:58.512988 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-18 22:18:58.562498 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-18 22:18:58.614999 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-18 22:18:58.678008 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-18 22:18:58.732774 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-18 22:18:58.784614 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-18 22:18:58.841362 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-18 22:18:58.898137 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-18 22:18:58.947243 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-18 22:18:59.000718 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-18 22:18:59.056019 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-18 22:18:59.106978 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-18 22:18:59.176434 INFO::Counting total values for each feature
2026-05-18 22:18:59.188888 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-18 22:18:59.24 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-18 22:18:59.298186 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-18 22:18:59.355106 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-18 22:18:59.382013 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-18 22:18:59.396107 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-18 22:18:59.399575 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-18 22:18:59.402629 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"
2026-05-18 22:18:59.412462 INFO::Writing function arguments to log file
2026-05-18 22:18:59.416069 INFO::Verifying options selected are valid
2026-05-18 22:18:59.416491 INFO::Determining format of input files
2026-05-18 22:18:59.417009 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-18 22:18:59.419428 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-18 22:18:59.420128 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-18 22:18:59.420843 INFO::Filter data based on min abundance and min prevalence
2026-05-18 22:18:59.421244 INFO::Total samples in data: 1595
2026-05-18 22:18:59.421619 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-18 22:18:59.423079 INFO::Total filtered features: 0
2026-05-18 22:18:59.423509 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-18 22:18:59.426031 INFO::Total filtered features with variance filtering: 0
2026-05-18 22:18:59.426452 INFO::Filtered feature names from variance filtering:
2026-05-18 22:18:59.426807 INFO::Running selected normalization method: NONE
2026-05-18 22:18:59.427147 INFO::Bypass z-score application to metadata
2026-05-18 22:18:59.427484 INFO::Running selected transform method: AST
2026-05-18 22:18:59.432829 INFO::Running selected analysis method: LM
2026-05-18 22:18:59.433449 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-18 22:18:59.481412 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-18 22:18:59.531659 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-18 22:18:59.581786 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-18 22:18:59.629331 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-18 22:18:59.677864 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-18 22:18:59.733504 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-18 22:18:59.782823 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-18 22:18:59.833683 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-18 22:18:59.884255 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-18 22:18:59.940901 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-18 22:18:59.991728 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-18 22:19:00.041471 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-18 22:19:00.094625 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-18 22:19:00.146016 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-18 22:19:00.197605 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-18 22:19:00.245746 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-18 22:19:00.301981 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-18 22:19:00.353775 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-18 22:19:00.403776 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-18 22:19:00.453206 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-18 22:19:00.508173 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-18 22:19:00.560664 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-18 22:19:00.610908 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-18 22:19:00.666256 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-18 22:19:00.719668 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-18 22:19:00.767937 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-18 22:19:00.817449 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-18 22:19:00.869173 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-18 22:19:00.915082 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-18 22:19:00.963454 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-18 22:19:01.012907 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-18 22:19:01.067995 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-18 22:19:01.115371 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-18 22:19:01.168056 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-18 22:19:01.220054 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-18 22:19:01.277083 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-18 22:19:01.3296 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-18 22:19:01.386125 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-18 22:19:01.43166 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-18 22:19:01.478555 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-18 22:19:01.529073 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-18 22:19:01.57761 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-18 22:19:01.628191 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-18 22:19:01.682455 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-18 22:19:01.732608 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-18 22:19:01.786022 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-18 22:19:01.837502 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-18 22:19:01.892248 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-18 22:19:01.945847 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-18 22:19:01.991679 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-18 22:19:02.044753 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-18 22:19:02.104847 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-18 22:19:02.151397 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-18 22:19:02.203195 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-18 22:19:02.257035 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-18 22:19:02.316608 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-18 22:19:02.368126 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-18 22:19:02.417725 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-18 22:19:02.473551 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-18 22:19:02.522127 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-18 22:19:02.571943 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-18 22:19:02.618442 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-18 22:19:02.670919 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-18 22:19:02.719733 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-18 22:19:02.76712 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-18 22:19:02.814949 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-18 22:19:02.867017 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-18 22:19:02.914597 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-18 22:19:02.966563 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-18 22:19:03.01909 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-18 22:19:03.073835 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-18 22:19:03.092 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-18 22:19:03.144184 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-18 22:19:03.193748 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-18 22:19:03.250135 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-18 22:19:03.298313 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-18 22:19:03.348109 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-18 22:19:03.397892 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-18 22:19:03.455293 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-18 22:19:03.508362 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-18 22:19:03.559753 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-18 22:19:03.619277 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-18 22:19:03.668866 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-18 22:19:03.722385 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-18 22:19:03.769976 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-18 22:19:03.823292 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-18 22:19:03.87419 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-18 22:19:03.934481 INFO::Counting total values for each feature
2026-05-18 22:19:03.947686 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-18 22:19:03.996561 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-18 22:19:04.045415 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-18 22:19:04.103054 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-18 22:19:04.139048 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-18 22:19:04.17351 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-18 22:19:04.176821 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-18 22:19:04.179371 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
10.961 0.197 11.169
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 39.606 | 0.493 | 40.194 | |