Sagun Maharjan
| Snapshot Date: 2026-04-28 14:14 -0400 (Tue, 28 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0616fc9 |
| git_last_commit_date: 2026-04-28 08:50:35 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-29 10:15 -0400 (Wed, 29 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4694 |
| 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 1197/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.26.0 (landing page) Sagun Maharjan
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2026-04-28 22:07:50 -0400 (Tue, 28 Apr 2026) |
| EndedAt: 2026-04-28 22:09:00 -0400 (Tue, 28 Apr 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-04-29 02:07:50 UTC
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.26.0’
* 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 39.971 0.52 40.607
* 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-3.23-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 ‘1.26.0’ ** 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 (2026-04-24 r89963) -- "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"
2026-04-28 22:08:46.010297 INFO::Writing function arguments to log file
2026-04-28 22:08:46.022294 INFO::Verifying options selected are valid
2026-04-28 22:08:46.036977 INFO::Determining format of input files
2026-04-28 22:08:46.037847 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-28 22:08:46.040671 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-28 22:08:46.041415 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-28 22:08:46.045471 INFO::Filter data based on min abundance and min prevalence
2026-04-28 22:08:46.046086 INFO::Total samples in data: 1595
2026-04-28 22:08:46.046536 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-28 22:08:46.048217 INFO::Total filtered features: 0
2026-04-28 22:08:46.048753 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-28 22:08:46.051856 INFO::Total filtered features with variance filtering: 0
2026-04-28 22:08:46.052392 INFO::Filtered feature names from variance filtering:
2026-04-28 22:08:46.052853 INFO::Running selected normalization method: TSS
2026-04-28 22:08:46.451843 INFO::Bypass z-score application to metadata
2026-04-28 22:08:46.452564 INFO::Running selected transform method: AST
2026-04-28 22:08:46.462534 INFO::Running selected analysis method: LM
2026-04-28 22:08:46.710347 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-28 22:08:46.94509 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-28 22:08:47.014052 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-28 22:08:47.069431 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-28 22:08:47.125276 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-28 22:08:47.186612 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-28 22:08:47.243267 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-28 22:08:47.305621 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-28 22:08:47.365676 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-28 22:08:47.417923 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-28 22:08:47.469835 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-28 22:08:47.550022 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-28 22:08:47.600182 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-28 22:08:47.651225 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-28 22:08:47.703342 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-28 22:08:47.759179 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-28 22:08:47.808422 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-28 22:08:47.862922 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-28 22:08:47.917833 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-28 22:08:47.965007 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-28 22:08:48.015881 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-28 22:08:48.073002 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-28 22:08:48.126121 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-28 22:08:48.175135 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-28 22:08:48.233212 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-28 22:08:48.28634 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-28 22:08:48.336188 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-28 22:08:48.398464 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-28 22:08:48.45273 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-28 22:08:48.504908 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-28 22:08:48.559125 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-28 22:08:48.616678 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-28 22:08:48.671225 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-28 22:08:48.731968 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-28 22:08:48.782824 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-28 22:08:48.841101 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-28 22:08:48.892464 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-28 22:08:48.948233 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-28 22:08:49.003165 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-28 22:08:49.053416 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-28 22:08:49.116619 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-28 22:08:49.171507 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-28 22:08:49.22441 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-28 22:08:49.280284 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-28 22:08:49.332271 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-28 22:08:49.385138 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-28 22:08:49.442306 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-28 22:08:49.498814 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-28 22:08:49.549015 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-28 22:08:49.601539 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-28 22:08:49.64953 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-28 22:08:49.697397 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-28 22:08:49.754217 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-28 22:08:49.807321 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-28 22:08:49.856372 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-28 22:08:49.915536 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-28 22:08:49.972443 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-28 22:08:50.029772 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-28 22:08:50.085813 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-28 22:08:50.135845 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-28 22:08:50.192061 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-28 22:08:50.248301 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-28 22:08:50.306509 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-28 22:08:50.358379 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-28 22:08:50.410697 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-28 22:08:50.467607 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-28 22:08:50.520995 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-28 22:08:50.575484 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-28 22:08:50.629436 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-28 22:08:50.694945 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-28 22:08:50.751685 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-28 22:08:50.909967 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-28 22:08:50.962141 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-28 22:08:51.010575 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-28 22:08:51.060627 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-28 22:08:51.114759 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-28 22:08:51.164051 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-28 22:08:51.214298 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-28 22:08:51.271634 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-28 22:08:51.327287 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-28 22:08:51.378944 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-28 22:08:51.434219 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-28 22:08:51.488557 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-28 22:08:51.539083 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-28 22:08:51.592395 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-28 22:08:51.645911 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-28 22:08:51.696867 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-28 22:08:51.764945 INFO::Counting total values for each feature
2026-04-28 22:08:51.777204 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-28 22:08:51.824734 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-28 22:08:51.88072 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-28 22:08:51.936597 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-28 22:08:51.96341 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-28 22:08:51.977661 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-28 22:08:51.981017 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-28 22:08:51.988014 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"
2026-04-28 22:08:51.994128 INFO::Writing function arguments to log file
2026-04-28 22:08:51.997518 INFO::Verifying options selected are valid
2026-04-28 22:08:51.997937 INFO::Determining format of input files
2026-04-28 22:08:51.998493 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-28 22:08:52.000869 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-28 22:08:52.001347 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-04-28 22:08:52.002029 INFO::Filter data based on min abundance and min prevalence
2026-04-28 22:08:52.002431 INFO::Total samples in data: 1595
2026-04-28 22:08:52.0028 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-28 22:08:52.004308 INFO::Total filtered features: 0
2026-04-28 22:08:52.004731 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-28 22:08:52.007413 INFO::Total filtered features with variance filtering: 0
2026-04-28 22:08:52.0079 INFO::Filtered feature names from variance filtering:
2026-04-28 22:08:52.008313 INFO::Running selected normalization method: NONE
2026-04-28 22:08:52.008701 INFO::Bypass z-score application to metadata
2026-04-28 22:08:52.009057 INFO::Running selected transform method: AST
2026-04-28 22:08:52.01415 INFO::Running selected analysis method: LM
2026-04-28 22:08:52.014799 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-28 22:08:52.063714 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-28 22:08:52.115499 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-28 22:08:52.16776 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-28 22:08:52.217103 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-28 22:08:52.265304 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-28 22:08:52.319397 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-28 22:08:52.369762 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-28 22:08:52.416326 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-28 22:08:52.465944 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-28 22:08:52.521957 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-28 22:08:52.573237 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-28 22:08:52.621124 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-28 22:08:52.67072 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-28 22:08:52.725434 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-28 22:08:52.778367 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-28 22:08:52.833153 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-28 22:08:52.891203 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-28 22:08:52.941082 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-28 22:08:52.98754 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-28 22:08:53.038245 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-28 22:08:53.096645 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-28 22:08:53.147659 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-28 22:08:53.195419 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-28 22:08:53.246169 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-28 22:08:53.298401 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-28 22:08:53.346333 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-28 22:08:53.397296 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-28 22:08:53.448806 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-28 22:08:53.498262 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-28 22:08:53.550467 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-28 22:08:53.603282 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-28 22:08:53.66147 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-28 22:08:53.710347 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-28 22:08:53.761603 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-28 22:08:53.815967 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-28 22:08:53.869029 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-28 22:08:53.920921 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-28 22:08:53.974566 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-28 22:08:54.020035 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-28 22:08:54.065892 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-28 22:08:54.117559 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-28 22:08:54.16525 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-28 22:08:54.21693 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-28 22:08:54.27222 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-28 22:08:54.322856 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-28 22:08:54.376887 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-28 22:08:54.42923 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-28 22:08:54.481257 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-28 22:08:54.533892 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-28 22:08:54.577904 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-28 22:08:54.628976 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-28 22:08:54.684987 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-28 22:08:54.729589 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-28 22:08:54.776213 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-28 22:08:54.825251 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-28 22:08:54.880467 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-28 22:08:54.928128 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-28 22:08:54.976753 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-28 22:08:55.033706 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-28 22:08:55.081692 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-28 22:08:55.13111 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-28 22:08:55.179406 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-28 22:08:55.232952 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-28 22:08:55.284196 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-28 22:08:55.332456 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-28 22:08:55.385106 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-28 22:08:55.440435 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-28 22:08:55.490472 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-28 22:08:55.544978 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-28 22:08:55.601254 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-28 22:08:55.658955 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-28 22:08:55.677209 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-28 22:08:55.730453 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-28 22:08:55.783159 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-28 22:08:55.839065 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-28 22:08:55.888676 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-28 22:08:55.941538 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-28 22:08:55.993394 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-28 22:08:56.050041 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-28 22:08:56.099631 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-28 22:08:56.148148 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-28 22:08:56.209218 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-28 22:08:56.256302 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-28 22:08:56.303712 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-28 22:08:56.351386 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-28 22:08:56.404913 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-28 22:08:56.458954 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-28 22:08:56.521788 INFO::Counting total values for each feature
2026-04-28 22:08:56.534965 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-28 22:08:56.582411 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-28 22:08:56.629513 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-28 22:08:56.68442 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-28 22:08:56.719533 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-28 22:08:56.754581 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-28 22:08:56.757999 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-28 22:08:56.760345 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
11.004 0.201 11.237
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 39.971 | 0.520 | 40.607 | |