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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Maaslin2_1.26.0.tar.gz |
| StartedAt: 2026-04-29 01:56:44 -0400 (Wed, 29 Apr 2026) |
| EndedAt: 2026-04-29 02:02:10 -0400 (Wed, 29 Apr 2026) |
| EllapsedTime: 325.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Maaslin2_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-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: 2026-04-29 05:56:44 UTC
* 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 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 121.875 0.986 124.36
* 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-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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 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"
2026-04-29 01:59:18.95508 INFO::Writing function arguments to log file
2026-04-29 01:59:18.981865 INFO::Verifying options selected are valid
2026-04-29 01:59:19.016662 INFO::Determining format of input files
2026-04-29 01:59:19.018265 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-29 01:59:19.030378 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-29 01:59:19.031856 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-04-29 01:59:19.03425 INFO::Filter data based on min abundance and min prevalence
2026-04-29 01:59:19.03521 INFO::Total samples in data: 1595
2026-04-29 01:59:19.0361 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-29 01:59:19.039901 INFO::Total filtered features: 0
2026-04-29 01:59:19.040976 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-29 01:59:19.047 INFO::Total filtered features with variance filtering: 0
2026-04-29 01:59:19.047993 INFO::Filtered feature names from variance filtering:
2026-04-29 01:59:19.048883 INFO::Running selected normalization method: TSS
2026-04-29 01:59:20.117595 INFO::Bypass z-score application to metadata
2026-04-29 01:59:20.119056 INFO::Running selected transform method: AST
2026-04-29 01:59:20.136694 INFO::Running selected analysis method: LM
2026-04-29 01:59:20.744433 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-29 01:59:21.337039 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-29 01:59:21.502037 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-29 01:59:21.643598 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-29 01:59:21.784923 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-29 01:59:21.934594 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-29 01:59:22.070765 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-29 01:59:22.208581 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-29 01:59:22.321219 WARNING::Fitting problem for feature 8 a warning was issued
2026-04-29 01:59:22.463782 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-29 01:59:22.573362 WARNING::Fitting problem for feature 9 a warning was issued
2026-04-29 01:59:22.761653 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-29 01:59:22.901258 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-29 01:59:23.039011 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-29 01:59:23.173487 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-29 01:59:23.295665 WARNING::Fitting problem for feature 13 a warning was issued
2026-04-29 01:59:23.442027 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-29 01:59:23.582765 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-29 01:59:23.733401 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-29 01:59:23.870265 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-29 01:59:24.018719 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-29 01:59:24.199261 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-29 01:59:24.34694 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-29 01:59:24.493029 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-29 01:59:24.648225 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-29 01:59:24.789568 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-29 01:59:24.92578 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-29 01:59:25.076652 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-29 01:59:25.21637 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-29 01:59:25.35735 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-29 01:59:25.518729 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-29 01:59:25.699126 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-29 01:59:25.859361 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-29 01:59:25.999648 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-29 01:59:26.151389 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-29 01:59:26.302603 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-29 01:59:26.462508 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-29 01:59:26.610438 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-29 01:59:26.756546 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-29 01:59:26.901723 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-29 01:59:27.046862 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-29 01:59:27.182323 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-29 01:59:27.33213 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-29 01:59:27.470815 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-29 01:59:27.615022 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-29 01:59:27.759995 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-29 01:59:27.906113 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-29 01:59:28.040533 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-29 01:59:28.183507 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-29 01:59:28.327306 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-29 01:59:28.481995 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-29 01:59:28.620895 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-29 01:59:28.769575 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-29 01:59:28.909935 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-29 01:59:29.06086 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-29 01:59:29.225761 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-29 01:59:29.381533 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-29 01:59:29.513468 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-29 01:59:29.689608 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-29 01:59:29.843225 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-29 01:59:29.984124 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-29 01:59:30.135119 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-29 01:59:30.274599 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-29 01:59:30.408027 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-29 01:59:30.79679 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-29 01:59:30.934569 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-29 01:59:31.07126 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-29 01:59:31.211979 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-29 01:59:31.357076 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-29 01:59:31.495639 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-29 01:59:31.622254 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-29 01:59:31.771459 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-29 01:59:31.931116 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-29 01:59:32.079402 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-29 01:59:32.220356 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-29 01:59:32.371772 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-29 01:59:32.505555 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-29 01:59:32.644318 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-29 01:59:32.79447 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-29 01:59:32.930867 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-29 01:59:33.070858 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-29 01:59:33.217927 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-29 01:59:33.371632 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-29 01:59:33.512119 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-29 01:59:33.660478 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-29 01:59:33.80567 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-29 01:59:33.949209 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-29 01:59:34.087639 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-29 01:59:34.221909 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-29 01:59:34.368111 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-29 01:59:34.552433 INFO::Counting total values for each feature
2026-04-29 01:59:34.583041 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-04-29 01:59:34.677859 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-04-29 01:59:34.774744 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-04-29 01:59:34.874113 INFO::Writing residuals to file output/fits/residuals.rds
2026-04-29 01:59:34.923281 INFO::Writing fitted values to file output/fits/fitted.rds
2026-04-29 01:59:34.950958 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-04-29 01:59:34.956501 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-04-29 01:59:34.961829 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"
2026-04-29 01:59:34.97507 INFO::Writing function arguments to log file
2026-04-29 01:59:34.981305 INFO::Verifying options selected are valid
2026-04-29 01:59:34.982324 INFO::Determining format of input files
2026-04-29 01:59:34.98355 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-29 01:59:34.988743 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-04-29 01:59:34.989849 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-04-29 01:59:34.991539 INFO::Filter data based on min abundance and min prevalence
2026-04-29 01:59:34.992472 INFO::Total samples in data: 1595
2026-04-29 01:59:34.993396 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-04-29 01:59:34.997188 INFO::Total filtered features: 0
2026-04-29 01:59:34.998177 INFO::Filtered feature names from abundance and prevalence filtering:
2026-04-29 01:59:35.012053 INFO::Total filtered features with variance filtering: 0
2026-04-29 01:59:35.013208 INFO::Filtered feature names from variance filtering:
2026-04-29 01:59:35.014089 INFO::Running selected normalization method: NONE
2026-04-29 01:59:35.014974 INFO::Bypass z-score application to metadata
2026-04-29 01:59:35.015839 INFO::Running selected transform method: AST
2026-04-29 01:59:35.030397 INFO::Running selected analysis method: LM
2026-04-29 01:59:35.031936 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-04-29 01:59:35.164435 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-04-29 01:59:35.30272 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-04-29 01:59:35.444144 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-04-29 01:59:35.575391 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-04-29 01:59:35.709769 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-04-29 01:59:35.857954 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-04-29 01:59:35.999409 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-04-29 01:59:36.131718 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-04-29 01:59:36.267475 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-04-29 01:59:36.42029 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-04-29 01:59:36.532014 WARNING::Fitting problem for feature 11 a warning was issued
2026-04-29 01:59:36.67901 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-04-29 01:59:36.808232 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-04-29 01:59:36.948553 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-04-29 01:59:37.081988 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-04-29 01:59:37.25033 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-04-29 01:59:37.375906 WARNING::Fitting problem for feature 16 a warning was issued
2026-04-29 01:59:37.510008 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-04-29 01:59:37.650826 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-04-29 01:59:37.791453 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-04-29 01:59:37.919006 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-04-29 01:59:38.050451 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-04-29 01:59:38.188184 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-04-29 01:59:38.324212 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-04-29 01:59:38.454349 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-04-29 01:59:38.599621 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-04-29 01:59:38.731609 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-04-29 01:59:38.862442 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-04-29 01:59:39.005885 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-04-29 01:59:39.135467 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-04-29 01:59:39.25888 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-04-29 01:59:39.396851 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-04-29 01:59:39.528704 INFO::Fitting model to feature number 32, Prevotella.copri
2026-04-29 01:59:39.659917 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-04-29 01:59:39.792504 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-04-29 01:59:39.924096 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-04-29 01:59:40.058665 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-04-29 01:59:40.190409 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-04-29 01:59:40.324829 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-04-29 01:59:40.480113 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-04-29 01:59:40.605873 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-04-29 01:59:40.747663 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-04-29 01:59:40.906257 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-04-29 01:59:41.040363 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-04-29 01:59:41.180606 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-04-29 01:59:41.322158 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-04-29 01:59:41.467647 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-04-29 01:59:41.602794 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-04-29 01:59:41.731377 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-04-29 01:59:41.869239 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-04-29 01:59:42.007356 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-04-29 01:59:42.129196 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-04-29 01:59:42.26161 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-04-29 01:59:42.384388 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-04-29 01:59:42.512898 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-04-29 01:59:42.640337 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-04-29 01:59:42.776212 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-04-29 01:59:42.925586 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-04-29 01:59:43.056467 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-04-29 01:59:43.188789 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-04-29 01:59:43.32275 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-04-29 01:59:43.458719 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-04-29 01:59:43.588542 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-04-29 01:59:43.720739 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-04-29 01:59:43.856621 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-04-29 01:59:43.999896 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-04-29 01:59:44.131503 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-04-29 01:59:44.264242 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-04-29 01:59:44.375803 WARNING::Fitting problem for feature 67 a warning was issued
2026-04-29 01:59:44.523666 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-04-29 01:59:44.658042 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-04-29 01:59:44.799179 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-04-29 01:59:44.95576 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-04-29 01:59:45.093502 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-04-29 01:59:45.142457 WARNING::Fitting problem for feature 72 a warning was issued
2026-04-29 01:59:45.286962 INFO::Fitting model to feature number 73, Dialister.invisus
2026-04-29 01:59:45.428617 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-04-29 01:59:45.559083 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-04-29 01:59:45.688347 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-04-29 01:59:45.829237 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-04-29 01:59:45.960148 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-04-29 01:59:46.096178 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-04-29 01:59:46.232254 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-04-29 01:59:46.366639 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-04-29 01:59:46.504984 INFO::Fitting model to feature number 82, Escherichia.coli
2026-04-29 01:59:46.634703 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-04-29 01:59:46.770211 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-04-29 01:59:46.897457 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-04-29 01:59:47.028144 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-04-29 01:59:47.168347 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-04-29 01:59:47.326706 INFO::Counting total values for each feature
2026-04-29 01:59:47.349391 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-04-29 01:59:47.443337 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-04-29 01:59:47.537264 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-04-29 01:59:47.645019 INFO::Writing residuals to file output2/fits/residuals.rds
2026-04-29 01:59:47.7102 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-04-29 01:59:47.773006 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-04-29 01:59:47.778762 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-04-29 01:59:47.783372 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
29.423 0.545 29.960
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 121.875 | 0.986 | 124.360 | |