Sagun Maharjan
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 05f7fa4 |
| git_last_commit_date: 2026-02-27 02:44:53 -0400 (Fri, 27 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1189/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.25.1 (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 | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Maaslin2 |
| Version: 1.25.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.25.1.tar.gz |
| StartedAt: 2026-04-17 04:36:10 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 04:40:39 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 268.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.25.1’
* 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 loading without being on the library search path ... 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 172.815 1.808 174.99
* 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
‘/home/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.25.1’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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"
2026-04-17 04:39:49.560215 INFO::Writing function arguments to log file
2026-04-17 04:39:49.61532 INFO::Verifying options selected are valid
2026-04-17 04:39:49.659899 INFO::Determining format of input files
2026-04-17 04:39:49.661918 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-17 04:39:49.669759 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-17 04:39:49.6717 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-17 04:39:49.675093 INFO::Filter data based on min abundance and min prevalence
2026-04-17 04:39:49.676362 INFO::Total samples in data: 1595
2026-04-17 04:39:49.677586 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-17 04:39:49.696146 INFO::Total filtered features: 0
2026-04-17 04:39:49.698004 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-17 04:39:49.725466 INFO::Total filtered features with variance filtering: 0
2026-04-17 04:39:49.727159 INFO::Filtered feature names from variance filtering:
2026-04-17 04:39:49.728424 INFO::Running selected normalization method: TSS
2026-04-17 04:39:51.280005 INFO::Bypass z-score application to metadata
2026-04-17 04:39:51.28179 INFO::Running selected transform method: AST
2026-04-17 04:39:51.306972 INFO::Running selected analysis method: LM
2026-04-17 04:39:52.005114 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-17 04:39:52.968939 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-17 04:39:53.250149 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-17 04:39:53.485902 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-17 04:39:53.733492 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-17 04:39:53.998288 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-17 04:39:54.229292 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-17 04:39:54.484025 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-17 04:39:54.756255 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-17 04:39:54.989487 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-17 04:39:55.213043 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-17 04:39:55.517203 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-17 04:39:55.746988 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-17 04:39:55.955688 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-17 04:39:56.215988 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-17 04:39:56.441264 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-17 04:39:56.672561 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-17 04:39:56.918243 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-17 04:39:57.165657 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-17 04:39:57.399324 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-17 04:39:57.638492 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-17 04:39:57.864256 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-17 04:39:58.090558 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-17 04:39:58.334186 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-17 04:39:58.562883 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-17 04:39:58.805989 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-17 04:39:59.058952 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-17 04:39:59.275641 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-17 04:39:59.521967 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-17 04:39:59.755859 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-17 04:40:00.004156 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-17 04:40:00.260487 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-17 04:40:00.521089 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-17 04:40:00.768994 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-17 04:40:01.006172 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-17 04:40:01.225625 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-17 04:40:01.465708 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-17 04:40:01.692691 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-17 04:40:01.9469 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-17 04:40:02.172933 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-17 04:40:02.407709 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-17 04:40:02.642596 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-17 04:40:02.884161 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-17 04:40:03.127011 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-17 04:40:03.386259 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-17 04:40:03.605167 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-17 04:40:03.833774 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-17 04:40:04.088123 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-17 04:40:04.342765 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-17 04:40:04.575351 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-17 04:40:05.131053 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-17 04:40:05.350873 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-17 04:40:05.578104 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-17 04:40:05.813579 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-17 04:40:06.053049 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-17 04:40:06.276294 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-17 04:40:06.519541 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-17 04:40:06.784257 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-17 04:40:07.007252 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-17 04:40:07.24503 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-17 04:40:07.484159 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-17 04:40:07.704199 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-17 04:40:07.933971 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-17 04:40:08.16546 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-17 04:40:08.407088 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-17 04:40:08.630569 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-17 04:40:08.855907 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-17 04:40:09.082652 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-17 04:40:09.324489 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-17 04:40:09.564953 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-17 04:40:09.815936 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-17 04:40:10.071054 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-17 04:40:10.290519 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-17 04:40:10.5167 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-17 04:40:10.74047 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-17 04:40:10.978238 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-17 04:40:11.210581 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-17 04:40:11.449739 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-17 04:40:12.026472 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-17 04:40:12.275324 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-17 04:40:12.524104 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-17 04:40:12.755474 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-17 04:40:13.006959 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-17 04:40:13.243106 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-17 04:40:13.467657 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-17 04:40:13.712166 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-17 04:40:13.939908 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-17 04:40:14.16211 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-17 04:40:14.462365 INFO::Counting total values for each feature
2026-04-17 04:40:14.512605 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-17 04:40:14.628807 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-17 04:40:14.747734 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-17 04:40:14.868916 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-17 04:40:14.925338 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-17 04:40:14.956615 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-17 04:40:14.963396 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-17 04:40:14.970228 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"
2026-04-17 04:40:14.987556 INFO::Writing function arguments to log file
2026-04-17 04:40:14.995664 INFO::Verifying options selected are valid
2026-04-17 04:40:14.997093 INFO::Determining format of input files
2026-04-17 04:40:14.998772 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-17 04:40:15.006771 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-17 04:40:15.008503 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-04-17 04:40:15.010905 INFO::Filter data based on min abundance and min prevalence
2026-04-17 04:40:15.012207 INFO::Total samples in data: 1595
2026-04-17 04:40:15.013471 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-17 04:40:15.0234 INFO::Total filtered features: 0
2026-04-17 04:40:15.025045 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-17 04:40:15.052431 INFO::Total filtered features with variance filtering: 0
2026-04-17 04:40:15.054053 INFO::Filtered feature names from variance filtering:
2026-04-17 04:40:15.0553 INFO::Running selected normalization method: NONE
2026-04-17 04:40:15.056488 INFO::Bypass z-score application to metadata
2026-04-17 04:40:15.057711 INFO::Running selected transform method: AST
2026-04-17 04:40:15.080906 INFO::Running selected analysis method: LM
2026-04-17 04:40:15.082986 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-17 04:40:15.315185 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-17 04:40:15.531653 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-17 04:40:15.735347 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-17 04:40:15.958712 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-17 04:40:16.207393 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-17 04:40:16.461425 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-17 04:40:16.686105 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-17 04:40:16.914309 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-17 04:40:17.089448 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-17 04:40:17.322396 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-17 04:40:17.542576 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-17 04:40:17.768784 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-17 04:40:17.975612 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-17 04:40:18.151571 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-17 04:40:18.374309 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-17 04:40:18.598701 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-17 04:40:18.818406 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-17 04:40:18.989269 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-17 04:40:19.20164 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-17 04:40:19.427696 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-17 04:40:19.640217 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-17 04:40:19.842365 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-17 04:40:20.384415 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-17 04:40:20.598172 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-17 04:40:20.813298 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-17 04:40:21.017858 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-17 04:40:21.243381 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-17 04:40:21.455547 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-17 04:40:21.665677 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-17 04:40:21.87966 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-17 04:40:22.09723 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-17 04:40:22.300909 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-17 04:40:22.51208 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-17 04:40:22.730888 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-17 04:40:22.943685 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-17 04:40:23.149422 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-17 04:40:23.358732 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-17 04:40:23.577334 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-17 04:40:23.792176 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-17 04:40:24.003578 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-17 04:40:24.213356 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-17 04:40:24.423312 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-17 04:40:24.625545 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-17 04:40:24.833257 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-17 04:40:25.077314 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-17 04:40:25.297752 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-17 04:40:25.524676 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-17 04:40:25.743631 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-17 04:40:25.973461 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-17 04:40:26.178157 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-17 04:40:26.392362 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-17 04:40:26.6021 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-17 04:40:26.809804 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-17 04:40:27.02212 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-17 04:40:27.220052 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-17 04:40:27.415328 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-17 04:40:27.632479 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-17 04:40:27.839081 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-17 04:40:28.05285 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-17 04:40:28.271768 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-17 04:40:28.479948 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-17 04:40:28.696721 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-17 04:40:28.902507 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-17 04:40:29.123726 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-17 04:40:29.329948 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-17 04:40:29.541782 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-17 04:40:29.752644 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-17 04:40:29.976168 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-17 04:40:30.193783 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-17 04:40:30.416466 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-17 04:40:30.655094 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-17 04:40:30.884692 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-17 04:40:31.114504 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-17 04:40:31.327435 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-17 04:40:31.401577 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-17 04:40:31.626222 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-17 04:40:31.839563 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-17 04:40:32.054914 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-17 04:40:32.275413 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-17 04:40:32.492694 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-17 04:40:32.703622 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-17 04:40:32.920798 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-17 04:40:33.154723 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-17 04:40:33.363198 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-17 04:40:33.582756 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-17 04:40:33.791255 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-17 04:40:34.008998 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-17 04:40:34.216825 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-17 04:40:34.433766 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-17 04:40:34.65556 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-17 04:40:34.923801 INFO::Counting total values for each feature
2026-04-17 04:40:34.96175 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-17 04:40:35.076809 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-17 04:40:35.191601 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-17 04:40:35.313271 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-17 04:40:35.389327 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-17 04:40:35.461585 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-17 04:40:35.468328 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-17 04:40:35.474104 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
46.648 0.654 47.403
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 172.815 | 1.808 | 174.990 | |