Sagun Maharjan
| Snapshot Date: 2026-05-06 13:45 -0400 (Wed, 06 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 2026-05-07 11:33 -0400 (Thu, 07 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" | 4879 |
| 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 1174/2366 | 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: 2026-05-07 01:24:57 -0400 (Thu, 07 May 2026) |
| EndedAt: 2026-05-07 01:30:20 -0400 (Thu, 07 May 2026) |
| EllapsedTime: 322.4 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: 2026-05-07 05:24:57 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 120.158 0.969 121.451
* 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"
2026-05-07 01:27:29.017794 INFO::Writing function arguments to log file
2026-05-07 01:27:29.042694 INFO::Verifying options selected are valid
2026-05-07 01:27:29.075657 INFO::Determining format of input files
2026-05-07 01:27:29.077288 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-07 01:27:29.088853 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-07 01:27:29.090335 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-07 01:27:29.092777 INFO::Filter data based on min abundance and min prevalence
2026-05-07 01:27:29.093687 INFO::Total samples in data: 1595
2026-05-07 01:27:29.094535 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-07 01:27:29.098115 INFO::Total filtered features: 0
2026-05-07 01:27:29.09913 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-07 01:27:29.105047 INFO::Total filtered features with variance filtering: 0
2026-05-07 01:27:29.106057 INFO::Filtered feature names from variance filtering:
2026-05-07 01:27:29.106915 INFO::Running selected normalization method: TSS
2026-05-07 01:27:30.145131 INFO::Bypass z-score application to metadata
2026-05-07 01:27:30.146429 INFO::Running selected transform method: AST
2026-05-07 01:27:30.164154 INFO::Running selected analysis method: LM
2026-05-07 01:27:30.784104 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-07 01:27:31.401306 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-07 01:27:31.571089 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-07 01:27:31.7158 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-07 01:27:31.858595 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-07 01:27:32.010684 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-07 01:27:32.149758 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-07 01:27:32.289234 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-07 01:27:32.404415 WARNING::Fitting problem for feature 8 a warning was issued
2026-05-07 01:27:32.549253 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-07 01:27:32.658404 WARNING::Fitting problem for feature 9 a warning was issued
2026-05-07 01:27:32.852563 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-07 01:27:32.991797 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-07 01:27:33.133473 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-07 01:27:33.271691 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-07 01:27:33.396045 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-07 01:27:33.544846 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-07 01:27:33.689825 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-07 01:27:33.844086 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-07 01:27:33.984526 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-07 01:27:34.142674 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-07 01:27:34.311393 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-07 01:27:34.457182 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-07 01:27:34.59802 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-07 01:27:34.742756 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-07 01:27:34.882475 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-07 01:27:35.016928 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-07 01:27:35.163763 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-07 01:27:35.304229 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-07 01:27:35.439301 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-07 01:27:35.592117 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-07 01:27:35.735522 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-07 01:27:35.886115 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-07 01:27:36.023861 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-07 01:27:36.170549 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-07 01:27:36.321246 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-07 01:27:36.473769 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-07 01:27:36.621318 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-07 01:27:36.766263 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-07 01:27:36.916961 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-07 01:27:37.062392 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-07 01:27:37.193922 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-07 01:27:37.335516 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-07 01:27:37.479858 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-07 01:27:37.627925 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-07 01:27:37.78227 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-07 01:27:37.933713 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-07 01:27:38.071603 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-07 01:27:38.21633 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-07 01:27:38.36096 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-07 01:27:38.517693 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-07 01:27:38.660091 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-07 01:27:38.810485 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-07 01:27:38.952293 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-07 01:27:39.111804 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-07 01:27:39.280675 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-07 01:27:39.441904 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-07 01:27:39.578669 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-07 01:27:39.770442 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-07 01:27:39.927727 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-07 01:27:40.076421 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-07 01:27:40.229254 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-07 01:27:40.365073 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-07 01:27:40.499139 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-07 01:27:40.898203 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-07 01:27:41.034822 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-07 01:27:41.170687 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-07 01:27:41.309287 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-07 01:27:41.451764 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-07 01:27:41.590833 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-07 01:27:41.719556 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-07 01:27:41.886337 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-07 01:27:42.041088 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-07 01:27:42.190765 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-07 01:27:42.333415 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-07 01:27:42.657625 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-07 01:27:42.921785 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-07 01:27:43.143072 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-07 01:27:44.449107 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-07 01:27:45.831728 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-07 01:27:46.605606 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-07 01:27:46.772766 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-07 01:27:46.926571 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-07 01:27:47.068619 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-07 01:27:47.211634 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-07 01:27:47.349453 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-07 01:27:47.490962 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-07 01:27:47.630047 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-07 01:27:47.764117 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-07 01:27:47.915659 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-07 01:27:48.128178 INFO::Counting total values for each feature
2026-05-07 01:27:48.165495 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-07 01:27:48.262804 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-07 01:27:48.361575 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-07 01:27:48.463429 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-07 01:27:48.51228 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-07 01:27:48.539711 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-07 01:27:48.54531 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-07 01:27:48.550838 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"
2026-05-07 01:27:48.566199 INFO::Writing function arguments to log file
2026-05-07 01:27:48.573181 INFO::Verifying options selected are valid
2026-05-07 01:27:48.574367 INFO::Determining format of input files
2026-05-07 01:27:48.575778 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-07 01:27:48.581715 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-07 01:27:48.583037 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-07 01:27:48.585024 INFO::Filter data based on min abundance and min prevalence
2026-05-07 01:27:48.586116 INFO::Total samples in data: 1595
2026-05-07 01:27:48.587169 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-07 01:27:48.591543 INFO::Total filtered features: 0
2026-05-07 01:27:48.59265 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-07 01:27:48.613234 INFO::Total filtered features with variance filtering: 0
2026-05-07 01:27:48.614459 INFO::Filtered feature names from variance filtering:
2026-05-07 01:27:48.615327 INFO::Running selected normalization method: NONE
2026-05-07 01:27:48.616205 INFO::Bypass z-score application to metadata
2026-05-07 01:27:48.617051 INFO::Running selected transform method: AST
2026-05-07 01:27:48.631621 INFO::Running selected analysis method: LM
2026-05-07 01:27:48.633238 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-07 01:27:48.769777 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-07 01:27:48.904336 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-07 01:27:49.040923 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-07 01:27:49.17035 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-07 01:27:49.299465 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-07 01:27:49.445246 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-07 01:27:49.577861 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-07 01:27:49.706786 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-07 01:27:49.843556 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-07 01:27:49.990787 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-07 01:27:50.104311 WARNING::Fitting problem for feature 11 a warning was issued
2026-05-07 01:27:50.252907 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-07 01:27:50.379684 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-07 01:27:50.519929 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-07 01:27:50.650888 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-07 01:27:50.78925 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-07 01:27:50.898284 WARNING::Fitting problem for feature 16 a warning was issued
2026-05-07 01:27:51.028421 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-07 01:27:51.165048 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-07 01:27:51.539161 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-07 01:27:51.672246 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-07 01:27:51.810805 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-07 01:27:51.952035 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-07 01:27:52.100249 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-07 01:27:52.229592 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-07 01:27:52.36455 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-07 01:27:52.495244 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-07 01:27:52.630075 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-07 01:27:52.766356 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-07 01:27:52.895154 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-07 01:27:53.026836 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-07 01:27:53.158087 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-07 01:27:53.291927 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-07 01:27:53.427085 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-07 01:27:53.560044 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-07 01:27:53.691022 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-07 01:27:53.819856 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-07 01:27:53.953608 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-07 01:27:54.095621 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-07 01:27:54.228044 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-07 01:27:54.353659 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-07 01:27:54.481529 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-07 01:27:54.614809 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-07 01:27:54.741242 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-07 01:27:54.877319 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-07 01:27:55.017355 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-07 01:27:55.147872 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-07 01:27:55.28159 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-07 01:27:55.413937 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-07 01:27:55.56107 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-07 01:27:55.691335 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-07 01:27:55.81382 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-07 01:27:55.950772 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-07 01:27:56.084163 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-07 01:27:56.206999 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-07 01:27:56.332678 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-07 01:27:56.464391 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-07 01:27:56.603357 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-07 01:27:56.734937 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-07 01:27:56.86398 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-07 01:27:56.999337 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-07 01:27:57.136009 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-07 01:27:57.269234 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-07 01:27:57.39952 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-07 01:27:57.545461 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-07 01:27:57.679156 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-07 01:27:57.808598 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-07 01:27:57.941083 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-07 01:27:58.060319 WARNING::Fitting problem for feature 67 a warning was issued
2026-05-07 01:27:58.199987 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-07 01:27:58.330196 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-07 01:27:58.468969 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-07 01:27:58.618527 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-07 01:27:58.751719 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-07 01:27:58.79816 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-07 01:27:58.933671 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-07 01:27:59.076852 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-07 01:27:59.213509 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-07 01:27:59.348174 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-07 01:27:59.483889 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-07 01:27:59.62313 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-07 01:27:59.758869 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-07 01:27:59.892857 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-07 01:28:00.0235 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-07 01:28:00.166777 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-07 01:28:00.292541 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-07 01:28:00.420945 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-07 01:28:00.560333 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-07 01:28:00.690979 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-07 01:28:00.825702 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-07 01:28:00.987771 INFO::Counting total values for each feature
2026-05-07 01:28:01.017642 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-07 01:28:01.113851 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-07 01:28:01.210278 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-07 01:28:01.311076 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-07 01:28:01.37474 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-07 01:28:01.436533 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-07 01:28:01.441957 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-07 01:28:01.446185 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
32.089 0.579 33.562
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 120.158 | 0.969 | 121.451 | |