Sagun Maharjan
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 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 Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:33 -0400 (Wed, 06 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" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 | | ||||||||
| taishan | 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. |
| 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: 2026-05-06 01:15:31 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 01:20:58 -0400 (Wed, 06 May 2026) |
| EllapsedTime: 326.4 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: 2026-05-06 05:15:32 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 120.802 1.206 122.809
* 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"
2026-05-06 01:18:05.29594 INFO::Writing function arguments to log file
2026-05-06 01:18:05.321453 INFO::Verifying options selected are valid
2026-05-06 01:18:05.354885 INFO::Determining format of input files
2026-05-06 01:18:05.356462 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-06 01:18:05.36837 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-06 01:18:05.370226 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-05-06 01:18:05.372945 INFO::Filter data based on min abundance and min prevalence
2026-05-06 01:18:05.374059 INFO::Total samples in data: 1595
2026-05-06 01:18:05.37503 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-06 01:18:05.379202 INFO::Total filtered features: 0
2026-05-06 01:18:05.380569 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-06 01:18:05.38734 INFO::Total filtered features with variance filtering: 0
2026-05-06 01:18:05.388763 INFO::Filtered feature names from variance filtering:
2026-05-06 01:18:05.389791 INFO::Running selected normalization method: TSS
2026-05-06 01:18:06.488901 INFO::Bypass z-score application to metadata
2026-05-06 01:18:06.490294 INFO::Running selected transform method: AST
2026-05-06 01:18:06.507819 INFO::Running selected analysis method: LM
2026-05-06 01:18:07.160833 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-06 01:18:07.922047 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-06 01:18:08.101623 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-06 01:18:08.533457 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-06 01:18:10.261991 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-06 01:18:11.399915 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-06 01:18:11.681566 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-06 01:18:11.839963 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-06 01:18:11.963155 WARNING::Fitting problem for feature 8 a warning was issued
2026-05-06 01:18:12.115461 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-06 01:18:12.232302 WARNING::Fitting problem for feature 9 a warning was issued
2026-05-06 01:18:12.461353 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-06 01:18:12.614639 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-06 01:18:12.771813 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-06 01:18:12.920736 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-06 01:18:13.04746 WARNING::Fitting problem for feature 13 a warning was issued
2026-05-06 01:18:13.218524 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-06 01:18:13.38007 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-06 01:18:13.554975 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-06 01:18:13.715852 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-06 01:18:13.873043 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-06 01:18:14.03423 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-06 01:18:14.189682 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-06 01:18:14.340394 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-06 01:18:14.512961 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-06 01:18:14.669433 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-06 01:18:14.816254 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-06 01:18:14.980259 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-06 01:18:15.129086 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-06 01:18:15.27628 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-06 01:18:15.470399 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-06 01:18:15.637744 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-06 01:18:15.816805 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-06 01:18:15.967458 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-06 01:18:16.127762 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-06 01:18:16.292328 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-06 01:18:16.460021 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-06 01:18:16.625826 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-06 01:18:16.778845 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-06 01:18:16.928654 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-06 01:18:17.079887 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-06 01:18:17.218617 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-06 01:18:17.368934 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-06 01:18:17.518182 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-06 01:18:17.671022 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-06 01:18:17.822784 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-06 01:18:17.978108 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-06 01:18:18.133367 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-06 01:18:18.309574 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-06 01:18:18.472638 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-06 01:18:18.64528 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-06 01:18:18.805249 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-06 01:18:18.963713 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-06 01:18:19.111716 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-06 01:18:19.256291 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-06 01:18:19.414703 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-06 01:18:19.586321 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-06 01:18:19.730021 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-06 01:18:19.924217 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-06 01:18:20.085069 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-06 01:18:20.238899 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-06 01:18:20.394058 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-06 01:18:20.535251 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-06 01:18:20.677039 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-06 01:18:21.103443 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-06 01:18:21.245336 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-06 01:18:21.384454 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-06 01:18:21.526402 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-06 01:18:21.688572 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-06 01:18:21.837742 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-06 01:18:21.983126 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-06 01:18:22.145776 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-06 01:18:22.293818 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-06 01:18:22.44199 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-06 01:18:22.580217 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-06 01:18:22.732085 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-06 01:18:22.872304 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-06 01:18:23.015112 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-06 01:18:23.169716 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-06 01:18:23.322895 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-06 01:18:23.477775 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-06 01:18:23.635157 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-06 01:18:23.807229 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-06 01:18:23.953785 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-06 01:18:24.108302 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-06 01:18:24.257309 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-06 01:18:24.407875 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-06 01:18:24.552549 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-06 01:18:24.697539 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-06 01:18:24.858262 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-06 01:18:25.048292 INFO::Counting total values for each feature
2026-05-06 01:18:25.079765 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-05-06 01:18:25.174497 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-05-06 01:18:25.271245 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-05-06 01:18:25.371043 INFO::Writing residuals to file output/fits/residuals.rds
2026-05-06 01:18:25.420312 INFO::Writing fitted values to file output/fits/fitted.rds
2026-05-06 01:18:25.447789 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-05-06 01:18:25.453262 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-05-06 01:18:25.458558 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"
2026-05-06 01:18:25.472514 INFO::Writing function arguments to log file
2026-05-06 01:18:25.478792 INFO::Verifying options selected are valid
2026-05-06 01:18:25.479897 INFO::Determining format of input files
2026-05-06 01:18:25.481209 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-06 01:18:25.486821 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-05-06 01:18:25.488065 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-05-06 01:18:25.489886 INFO::Filter data based on min abundance and min prevalence
2026-05-06 01:18:25.490879 INFO::Total samples in data: 1595
2026-05-06 01:18:25.491838 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-05-06 01:18:25.495866 INFO::Total filtered features: 0
2026-05-06 01:18:25.496969 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-06 01:18:25.511828 INFO::Total filtered features with variance filtering: 0
2026-05-06 01:18:25.513122 INFO::Filtered feature names from variance filtering:
2026-05-06 01:18:25.514057 INFO::Running selected normalization method: NONE
2026-05-06 01:18:25.514956 INFO::Bypass z-score application to metadata
2026-05-06 01:18:25.515843 INFO::Running selected transform method: AST
2026-05-06 01:18:25.530503 INFO::Running selected analysis method: LM
2026-05-06 01:18:25.532131 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-05-06 01:18:25.667284 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-05-06 01:18:25.806312 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-05-06 01:18:25.944958 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-05-06 01:18:26.082485 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-05-06 01:18:26.235632 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-05-06 01:18:26.406054 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-05-06 01:18:26.547975 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-05-06 01:18:26.689207 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-05-06 01:18:26.841977 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-05-06 01:18:26.998194 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-05-06 01:18:27.115308 WARNING::Fitting problem for feature 11 a warning was issued
2026-05-06 01:18:27.261919 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-05-06 01:18:27.393676 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-05-06 01:18:27.53502 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-05-06 01:18:27.669613 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-05-06 01:18:27.814017 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-05-06 01:18:27.930951 WARNING::Fitting problem for feature 16 a warning was issued
2026-05-06 01:18:28.068899 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-05-06 01:18:28.22341 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-05-06 01:18:28.37934 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-05-06 01:18:28.516995 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-05-06 01:18:28.656643 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-05-06 01:18:28.801806 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-05-06 01:18:28.940974 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-05-06 01:18:29.073883 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-05-06 01:18:29.221517 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-05-06 01:18:29.356407 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-05-06 01:18:29.490947 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-05-06 01:18:29.640917 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-05-06 01:18:29.774875 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-05-06 01:18:29.908149 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-05-06 01:18:30.061954 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-05-06 01:18:30.200876 INFO::Fitting model to feature number 32, Prevotella.copri
2026-05-06 01:18:30.338278 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-05-06 01:18:30.47622 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-05-06 01:18:30.614357 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-05-06 01:18:30.753012 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-05-06 01:18:30.886853 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-05-06 01:18:31.025186 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-05-06 01:18:31.189799 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-05-06 01:18:31.314394 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-05-06 01:18:31.445245 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-05-06 01:18:31.587943 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-05-06 01:18:31.718938 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-05-06 01:18:31.85688 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-05-06 01:18:31.997109 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-05-06 01:18:32.172024 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-05-06 01:18:32.315755 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-05-06 01:18:32.456248 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-05-06 01:18:32.599174 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-05-06 01:18:32.74339 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-05-06 01:18:32.869219 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-05-06 01:18:33.007354 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-05-06 01:18:33.137468 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-05-06 01:18:33.273046 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-05-06 01:18:33.406322 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-05-06 01:18:33.549927 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-05-06 01:18:33.699107 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-05-06 01:18:33.836347 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-05-06 01:18:33.972943 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-05-06 01:18:34.114112 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-05-06 01:18:34.259158 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-05-06 01:18:34.396729 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-05-06 01:18:34.531327 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-05-06 01:18:34.683549 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-05-06 01:18:34.843576 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-05-06 01:18:34.982716 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-05-06 01:18:35.126297 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-05-06 01:18:35.24054 WARNING::Fitting problem for feature 67 a warning was issued
2026-05-06 01:18:35.39347 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-05-06 01:18:35.529816 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-05-06 01:18:35.674991 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-05-06 01:18:35.832769 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-05-06 01:18:35.97404 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-05-06 01:18:36.024152 WARNING::Fitting problem for feature 72 a warning was issued
2026-05-06 01:18:36.164331 INFO::Fitting model to feature number 73, Dialister.invisus
2026-05-06 01:18:36.311276 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-05-06 01:18:36.445606 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-05-06 01:18:36.57996 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-05-06 01:18:36.718574 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-05-06 01:18:36.867835 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-05-06 01:18:37.006001 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-05-06 01:18:37.148187 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-05-06 01:18:37.294222 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-05-06 01:18:37.437904 INFO::Fitting model to feature number 82, Escherichia.coli
2026-05-06 01:18:37.574136 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-05-06 01:18:37.717818 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-05-06 01:18:37.853631 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-05-06 01:18:37.992039 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-05-06 01:18:38.146332 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-05-06 01:18:38.309724 INFO::Counting total values for each feature
2026-05-06 01:18:38.332711 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-05-06 01:18:38.426403 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-05-06 01:18:38.520027 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-05-06 01:18:38.624961 INFO::Writing residuals to file output2/fits/residuals.rds
2026-05-06 01:18:38.689626 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-05-06 01:18:38.752077 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-05-06 01:18:38.757542 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-05-06 01:18:38.76197 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
32.730 0.850 34.615
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 120.802 | 1.206 | 122.809 | |