Sagun Maharjan
| Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 05f7fa4 |
| git_last_commit_date: 2026-02-27 02:44:53 -0400 (Fri, 27 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-14 11:34 -0400 (Sat, 14 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4050 |
| 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 1171/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.25.1 (landing page) Sagun Maharjan
| nebbiolo1 | Linux (Ubuntu 24.04.3 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: 1.25.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.25.1.tar.gz |
| StartedAt: 2026-03-13 19:09:50 -0400 (Fri, 13 Mar 2026) |
| EndedAt: 2026-03-13 19:11:08 -0400 (Fri, 13 Mar 2026) |
| EllapsedTime: 77.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-13 23:09:51 UTC
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.25.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 42.479 0.661 45.056
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.25.1’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Maaslin2)
Maaslin2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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"
2026-03-13 19:10:52.244106 INFO::Writing function arguments to log file
2026-03-13 19:10:52.261196 INFO::Verifying options selected are valid
2026-03-13 19:10:52.275286 INFO::Determining format of input files
2026-03-13 19:10:52.276094 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-13 19:10:52.278704 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-13 19:10:52.279293 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2026-03-13 19:10:52.2803 INFO::Filter data based on min abundance and min prevalence
2026-03-13 19:10:52.28068 INFO::Total samples in data: 1595
2026-03-13 19:10:52.281029 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-13 19:10:52.282989 INFO::Total filtered features: 0
2026-03-13 19:10:52.283433 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-13 19:10:52.287199 INFO::Total filtered features with variance filtering: 0
2026-03-13 19:10:52.287661 INFO::Filtered feature names from variance filtering:
2026-03-13 19:10:52.28801 INFO::Running selected normalization method: TSS
2026-03-13 19:10:52.714784 INFO::Bypass z-score application to metadata
2026-03-13 19:10:52.715346 INFO::Running selected transform method: AST
2026-03-13 19:10:52.721433 INFO::Running selected analysis method: LM
2026-03-13 19:10:53.003037 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-13 19:10:53.261224 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-13 19:10:53.332514 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-13 19:10:53.388333 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-13 19:10:53.447124 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-13 19:10:53.515316 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-13 19:10:53.577985 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-13 19:10:53.640802 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-13 19:10:53.709281 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-13 19:10:53.767942 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-13 19:10:53.830879 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-13 19:10:53.887509 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-13 19:10:53.971544 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-13 19:10:54.021605 WARNING::Fitting problem for feature 13 a warning was issued
2026-03-13 19:10:54.083077 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-13 19:10:54.146888 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-13 19:10:54.204721 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-13 19:10:54.263863 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-13 19:10:54.324741 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-13 19:10:54.380592 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-13 19:10:54.436077 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-13 19:10:54.49409 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-13 19:10:54.551147 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-13 19:10:54.606941 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-13 19:10:54.667658 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-13 19:10:54.732919 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-13 19:10:54.789839 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-13 19:10:54.846078 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-13 19:10:54.907762 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-13 19:10:54.964666 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-13 19:10:55.034325 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-13 19:10:55.093651 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-13 19:10:55.156066 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-13 19:10:55.211869 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-13 19:10:55.265816 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-13 19:10:55.320306 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-13 19:10:55.379504 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-13 19:10:55.435984 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-13 19:10:55.499105 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-13 19:10:55.554292 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-13 19:10:55.610091 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-13 19:10:55.669743 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-13 19:10:55.732257 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-13 19:10:55.788205 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-13 19:10:55.852198 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-13 19:10:55.90539 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-13 19:10:55.965393 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-13 19:10:56.024069 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-13 19:10:56.086283 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-13 19:10:56.144459 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-13 19:10:56.208001 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-13 19:10:56.261814 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-13 19:10:56.320827 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-13 19:10:56.379712 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-13 19:10:56.446465 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-13 19:10:56.499685 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-13 19:10:56.576593 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-13 19:10:56.636293 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-13 19:10:56.694426 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-13 19:10:56.76152 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-13 19:10:56.81773 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-13 19:10:56.874888 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-13 19:10:56.935234 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-13 19:10:56.993139 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-13 19:10:57.047394 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-13 19:10:57.225749 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-13 19:10:57.281865 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-13 19:10:57.336767 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-13 19:10:57.391204 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-13 19:10:57.458993 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-13 19:10:57.517167 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-13 19:10:57.586443 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-13 19:10:57.64942 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-13 19:10:57.707415 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-13 19:10:57.759267 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-13 19:10:57.814087 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-13 19:10:57.877842 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-13 19:10:57.939645 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-13 19:10:57.999646 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-13 19:10:58.059837 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-13 19:10:58.121945 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-13 19:10:58.184637 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-13 19:10:58.238644 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-13 19:10:58.29665 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-13 19:10:58.353085 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-13 19:10:58.415071 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-13 19:10:58.477494 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-13 19:10:58.530636 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-13 19:10:58.617657 INFO::Counting total values for each feature
2026-03-13 19:10:58.629222 INFO::Writing filtered data to file output/features/filtered_data.tsv
2026-03-13 19:10:58.684709 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2026-03-13 19:10:58.742155 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2026-03-13 19:10:58.811346 INFO::Writing residuals to file output/fits/residuals.rds
2026-03-13 19:10:58.842409 INFO::Writing fitted values to file output/fits/fitted.rds
2026-03-13 19:10:58.857179 INFO::Writing extracted random effects to file output/fits/ranef.rds
2026-03-13 19:10:58.860184 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2026-03-13 19:10:58.862907 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"
2026-03-13 19:10:58.86862 INFO::Writing function arguments to log file
2026-03-13 19:10:58.8708 INFO::Verifying options selected are valid
2026-03-13 19:10:58.871128 INFO::Determining format of input files
2026-03-13 19:10:58.87155 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-13 19:10:58.873751 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2026-03-13 19:10:58.87411 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2026-03-13 19:10:58.874706 INFO::Filter data based on min abundance and min prevalence
2026-03-13 19:10:58.874995 INFO::Total samples in data: 1595
2026-03-13 19:10:58.875274 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2026-03-13 19:10:58.87682 INFO::Total filtered features: 0
2026-03-13 19:10:58.87714 INFO::Filtered feature names from abundance and prevalence filtering:
2026-03-13 19:10:58.879964 INFO::Total filtered features with variance filtering: 0
2026-03-13 19:10:58.880305 INFO::Filtered feature names from variance filtering:
2026-03-13 19:10:58.880601 INFO::Running selected normalization method: NONE
2026-03-13 19:10:58.880885 INFO::Bypass z-score application to metadata
2026-03-13 19:10:58.88116 INFO::Running selected transform method: AST
2026-03-13 19:10:58.886965 INFO::Running selected analysis method: LM
2026-03-13 19:10:58.887597 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2026-03-13 19:10:58.945137 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2026-03-13 19:10:59.001352 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2026-03-13 19:10:59.065587 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2026-03-13 19:10:59.117416 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2026-03-13 19:10:59.301465 INFO::Fitting model to feature number 6, Bacteroides.caccae
2026-03-13 19:10:59.353369 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2026-03-13 19:10:59.408953 INFO::Fitting model to feature number 8, Bacteroides.dorei
2026-03-13 19:10:59.463579 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2026-03-13 19:10:59.523561 INFO::Fitting model to feature number 10, Bacteroides.faecis
2026-03-13 19:10:59.583696 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2026-03-13 19:10:59.638819 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2026-03-13 19:10:59.702303 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2026-03-13 19:10:59.757212 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2026-03-13 19:10:59.808627 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2026-03-13 19:10:59.874296 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2026-03-13 19:10:59.914422 WARNING::Fitting problem for feature 16 a warning was issued
2026-03-13 19:10:59.981632 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2026-03-13 19:11:00.04091 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2026-03-13 19:11:00.098024 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2026-03-13 19:11:00.147586 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2026-03-13 19:11:00.206878 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2026-03-13 19:11:00.263886 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2026-03-13 19:11:00.326138 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2026-03-13 19:11:00.382159 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2026-03-13 19:11:00.44154 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2026-03-13 19:11:00.494671 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2026-03-13 19:11:00.545898 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2026-03-13 19:11:00.607246 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2026-03-13 19:11:00.66847 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2026-03-13 19:11:00.716577 INFO::Fitting model to feature number 30, Paraprevotella.clara
2026-03-13 19:11:00.773471 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2026-03-13 19:11:00.824327 INFO::Fitting model to feature number 32, Prevotella.copri
2026-03-13 19:11:00.887546 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2026-03-13 19:11:00.939145 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2026-03-13 19:11:00.9975 INFO::Fitting model to feature number 35, Alistipes.putredinis
2026-03-13 19:11:01.051678 INFO::Fitting model to feature number 36, Alistipes.shahii
2026-03-13 19:11:01.107238 INFO::Fitting model to feature number 37, Alistipes.unclassified
2026-03-13 19:11:01.164144 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2026-03-13 19:11:01.217686 INFO::Fitting model to feature number 39, Clostridium.bolteae
2026-03-13 19:11:01.268015 INFO::Fitting model to feature number 40, Clostridium.citroniae
2026-03-13 19:11:01.330055 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2026-03-13 19:11:01.387571 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2026-03-13 19:11:01.443505 INFO::Fitting model to feature number 43, Clostridium.leptum
2026-03-13 19:11:01.500445 INFO::Fitting model to feature number 44, Clostridium.nexile
2026-03-13 19:11:01.559927 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2026-03-13 19:11:01.619325 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2026-03-13 19:11:01.673792 INFO::Fitting model to feature number 47, Eubacterium.eligens
2026-03-13 19:11:01.734282 INFO::Fitting model to feature number 48, Eubacterium.hallii
2026-03-13 19:11:01.785934 INFO::Fitting model to feature number 49, Eubacterium.rectale
2026-03-13 19:11:01.847134 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2026-03-13 19:11:01.892642 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2026-03-13 19:11:01.94776 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2026-03-13 19:11:01.996891 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2026-03-13 19:11:02.041887 WARNING::Fitting problem for feature 53 a warning was issued
2026-03-13 19:11:02.100653 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2026-03-13 19:11:02.150973 INFO::Fitting model to feature number 55, Ruminococcus.torques
2026-03-13 19:11:02.208414 INFO::Fitting model to feature number 56, Coprococcus.comes
2026-03-13 19:11:02.269342 INFO::Fitting model to feature number 57, Dorea.longicatena
2026-03-13 19:11:02.321979 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2026-03-13 19:11:02.370654 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2026-03-13 19:11:02.429753 INFO::Fitting model to feature number 60, Roseburia.hominis
2026-03-13 19:11:02.499014 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2026-03-13 19:11:02.549559 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2026-03-13 19:11:02.602778 INFO::Fitting model to feature number 63, Roseburia.unclassified
2026-03-13 19:11:02.652441 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2026-03-13 19:11:02.707809 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2026-03-13 19:11:02.757197 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2026-03-13 19:11:02.810246 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2026-03-13 19:11:02.865563 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2026-03-13 19:11:02.922796 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2026-03-13 19:11:02.980442 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2026-03-13 19:11:03.038261 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2026-03-13 19:11:03.091097 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2026-03-13 19:11:03.110883 WARNING::Fitting problem for feature 72 a warning was issued
2026-03-13 19:11:03.175584 INFO::Fitting model to feature number 73, Dialister.invisus
2026-03-13 19:11:03.232529 INFO::Fitting model to feature number 74, Veillonella.atypica
2026-03-13 19:11:03.296497 INFO::Fitting model to feature number 75, Veillonella.dispar
2026-03-13 19:11:03.372723 INFO::Fitting model to feature number 76, Veillonella.parvula
2026-03-13 19:11:03.445098 INFO::Fitting model to feature number 77, Veillonella.unclassified
2026-03-13 19:11:03.497123 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2026-03-13 19:11:03.559174 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2026-03-13 19:11:03.613061 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2026-03-13 19:11:03.671305 INFO::Fitting model to feature number 81, Bilophila.unclassified
2026-03-13 19:11:03.728998 INFO::Fitting model to feature number 82, Escherichia.coli
2026-03-13 19:11:03.77911 INFO::Fitting model to feature number 83, Escherichia.unclassified
2026-03-13 19:11:03.832266 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2026-03-13 19:11:03.890275 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2026-03-13 19:11:03.939093 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2026-03-13 19:11:04.002695 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2026-03-13 19:11:04.065006 INFO::Counting total values for each feature
2026-03-13 19:11:04.074509 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2026-03-13 19:11:04.129019 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2026-03-13 19:11:04.206805 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2026-03-13 19:11:04.268773 INFO::Writing residuals to file output2/fits/residuals.rds
2026-03-13 19:11:04.30805 INFO::Writing fitted values to file output2/fits/fitted.rds
2026-03-13 19:11:04.344688 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2026-03-13 19:11:04.347941 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2026-03-13 19:11:04.350216 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 4 | SKIP 0 | PASS 12 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
>
>
> proc.time()
user system elapsed
11.925 0.287 12.634
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 42.479 | 0.661 | 45.056 | |