Sagun Maharjan
| Snapshot Date: 2026-05-10 13:45 -0400 (Sun, 10 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 Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-11 11:33 -0400 (Mon, 11 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" | 4890 |
| 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 1181/2374 | 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 | | ||||||||
| 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: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings Maaslin2_1.27.0.tar.gz |
| StartedAt: 2026-05-11 01:32:51 -0400 (Mon, 11 May 2026) |
| EndedAt: 2026-05-11 01:38:12 -0400 (Mon, 11 May 2026) |
| EllapsedTime: 321.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings Maaslin2_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/Maaslin2.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-11 05:32:51 UTC
* 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 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 118.807 0.996 121.378
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.24-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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"
2026-05-11 01:35:26.024593 INFO::Writing function arguments to log file
2026-05-11 01:35:26.049182 INFO::Verifying options selected are valid
2026-05-11 01:35:26.082261 INFO::Determining format of input files
2026-05-11 01:35:26.083822 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-11 01:35:26.094923 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-11 01:35:26.096494 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-11 01:35:26.098903 INFO::Filter data based on min abundance and min prevalence
2026-05-11 01:35:26.099847 INFO::Total samples in data: 1595
2026-05-11 01:35:26.100723 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-11 01:35:26.10444 INFO::Total filtered features: 0
2026-05-11 01:35:26.105589 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-11 01:35:26.111724 INFO::Total filtered features with variance filtering: 0
2026-05-11 01:35:26.112825 INFO::Filtered feature names from variance filtering:
2026-05-11 01:35:26.113703 INFO::Running selected normalization method: TSS
2026-05-11 01:35:27.080868 INFO::Bypass z-score application to metadata
2026-05-11 01:35:27.082088 INFO::Running selected transform method: AST
2026-05-11 01:35:27.099559 INFO::Running selected analysis method: LM
2026-05-11 01:35:27.677074 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-11 01:35:28.281179 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-11 01:35:28.453572 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-11 01:35:28.594865 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-11 01:35:28.741204 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-11 01:35:28.895056 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-11 01:35:29.036729 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-11 01:35:29.177536 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-11 01:35:29.293268 WARNING::Fitting problem for feature 8 a warning was issued
2026-05-11 01:35:29.470737 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-11 01:35:29.589008 WARNING::Fitting problem for feature 9 a warning was issued
2026-05-11 01:35:29.808913 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-11 01:35:29.950728 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-11 01:35:30.090452 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-11 01:35:30.225982 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-11 01:35:30.35059 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-11 01:35:30.503931 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-11 01:35:30.64777 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-11 01:35:30.802234 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-11 01:35:30.940457 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-11 01:35:31.081833 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-11 01:35:31.227314 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-11 01:35:31.357105 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-11 01:35:31.490797 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-11 01:35:31.634933 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-11 01:35:31.786736 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-11 01:35:31.929828 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-11 01:35:32.083668 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-11 01:35:32.224612 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-11 01:35:32.362645 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-11 01:35:32.515432 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-11 01:35:32.656815 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-11 01:35:32.807492 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-11 01:35:32.944766 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-11 01:35:33.089438 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-11 01:35:33.235128 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-11 01:35:33.378321 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-11 01:35:33.521348 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-11 01:35:33.663029 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-11 01:35:33.806943 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-11 01:35:33.951776 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-11 01:35:34.084414 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-11 01:35:34.224573 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-11 01:35:34.378026 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-11 01:35:34.546241 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-11 01:35:34.698639 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-11 01:35:34.844951 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-11 01:35:34.984545 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-11 01:35:35.128322 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-11 01:35:35.269121 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-11 01:35:35.421608 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-11 01:35:35.560883 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-11 01:35:35.704066 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-11 01:35:35.844723 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-11 01:35:35.984097 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-11 01:35:36.1294 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-11 01:35:36.283732 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-11 01:35:36.422194 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-11 01:35:36.598257 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-11 01:35:36.752938 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-11 01:35:36.891676 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-11 01:35:37.044876 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-11 01:35:37.19892 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-11 01:35:37.353791 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-11 01:35:37.768095 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-11 01:35:37.908721 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-11 01:35:38.044844 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-11 01:35:38.185978 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-11 01:35:38.329493 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-11 01:35:38.470685 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-11 01:35:38.597808 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-11 01:35:38.748652 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-11 01:35:38.898752 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-11 01:35:39.045235 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-11 01:35:39.182074 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-11 01:35:39.326248 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-11 01:35:39.461095 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-11 01:35:39.599257 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-11 01:35:39.742651 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-11 01:35:39.876883 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-11 01:35:40.016587 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-11 01:35:40.164841 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-11 01:35:40.316479 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-11 01:35:40.453001 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-11 01:35:40.598714 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-11 01:35:40.739453 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-11 01:35:40.883818 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-11 01:35:41.023611 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-11 01:35:41.154358 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-11 01:35:41.297891 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-11 01:35:41.477135 INFO::Counting total values for each feature
2026-05-11 01:35:41.506963 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-11 01:35:41.603714 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-11 01:35:41.702303 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-11 01:35:41.802994 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-11 01:35:41.851608 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-11 01:35:41.878669 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-11 01:35:41.884026 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-11 01:35:41.889047 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"
2026-05-11 01:35:41.901872 INFO::Writing function arguments to log file
2026-05-11 01:35:41.907967 INFO::Verifying options selected are valid
2026-05-11 01:35:41.908952 INFO::Determining format of input files
2026-05-11 01:35:41.910168 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-11 01:35:41.91519 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-11 01:35:41.916276 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-11 01:35:41.917937 INFO::Filter data based on min abundance and min prevalence
2026-05-11 01:35:41.918848 INFO::Total samples in data: 1595
2026-05-11 01:35:41.919741 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-11 01:35:41.923196 INFO::Total filtered features: 0
2026-05-11 01:35:41.924159 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-11 01:35:41.937336 INFO::Total filtered features with variance filtering: 0
2026-05-11 01:35:41.93849 INFO::Filtered feature names from variance filtering:
2026-05-11 01:35:41.939361 INFO::Running selected normalization method: NONE
2026-05-11 01:35:41.940196 INFO::Bypass z-score application to metadata
2026-05-11 01:35:41.941033 INFO::Running selected transform method: AST
2026-05-11 01:35:41.955359 INFO::Running selected analysis method: LM
2026-05-11 01:35:41.956964 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-11 01:35:42.086868 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-11 01:35:42.220826 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-11 01:35:42.355155 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-11 01:35:42.508102 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-11 01:35:42.653848 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-11 01:35:42.815381 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-11 01:35:42.953007 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-11 01:35:43.082652 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-11 01:35:43.219701 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-11 01:35:43.370298 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-11 01:35:43.481859 WARNING::Fitting problem for feature 11 a warning was issued
2026-05-11 01:35:43.62641 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-11 01:35:43.754932 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-11 01:35:43.894249 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-11 01:35:44.027584 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-11 01:35:44.167536 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-11 01:35:44.279441 WARNING::Fitting problem for feature 16 a warning was issued
2026-05-11 01:35:44.417481 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-11 01:35:44.558177 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-11 01:35:44.696596 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-11 01:35:44.823182 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-11 01:35:44.956927 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-11 01:35:45.098454 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-11 01:35:45.231824 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-11 01:35:45.358233 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-11 01:35:45.502856 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-11 01:35:45.633948 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-11 01:35:45.763484 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-11 01:35:45.909541 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-11 01:35:46.044877 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-11 01:35:46.179677 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-11 01:35:46.328969 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-11 01:35:46.466743 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-11 01:35:46.60137 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-11 01:35:46.737154 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-11 01:35:46.871079 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-11 01:35:47.006225 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-11 01:35:47.135724 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-11 01:35:47.269646 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-11 01:35:47.42673 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-11 01:35:47.549055 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-11 01:35:47.677067 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-11 01:35:47.818702 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-11 01:35:47.944122 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-11 01:35:48.0801 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-11 01:35:48.217291 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-11 01:35:48.359764 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-11 01:35:48.492712 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-11 01:35:48.622387 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-11 01:35:48.758901 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-11 01:35:48.90068 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-11 01:35:49.022174 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-11 01:35:49.154063 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-11 01:35:49.274718 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-11 01:35:49.402345 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-11 01:35:49.527382 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-11 01:35:49.656748 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-11 01:35:49.800164 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-11 01:35:49.931545 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-11 01:35:50.058913 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-11 01:35:50.191112 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-11 01:35:50.324268 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-11 01:35:50.45377 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-11 01:35:50.578941 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-11 01:35:50.708517 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-11 01:35:50.847346 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-11 01:35:50.976642 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-11 01:35:51.108644 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-11 01:35:51.22543 WARNING::Fitting problem for feature 67 a warning was issued
2026-05-11 01:35:51.378319 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-11 01:35:51.510502 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-11 01:35:51.651917 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-11 01:35:51.804142 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-11 01:35:51.939133 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-11 01:35:51.986806 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-11 01:35:52.124754 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-11 01:35:52.263983 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-11 01:35:52.396161 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-11 01:35:52.528404 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-11 01:35:52.66521 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-11 01:35:52.810333 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-11 01:35:52.952676 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-11 01:35:53.095711 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-11 01:35:53.234012 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-11 01:35:53.373285 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-11 01:35:53.501674 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-11 01:35:53.637362 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-11 01:35:53.763369 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-11 01:35:53.89193 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-11 01:35:54.035586 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-11 01:35:54.195956 INFO::Counting total values for each feature
2026-05-11 01:35:54.218129 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-11 01:35:54.314312 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-11 01:35:54.410104 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-11 01:35:54.517087 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-11 01:35:54.581299 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-11 01:35:54.643573 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-11 01:35:54.649113 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-11 01:35:54.65354 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 7 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
30.821 0.664 31.829
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 118.807 | 0.996 | 121.378 | |