Lauren McIver
| Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: devel |
| git_last_commit: 43d70cc |
| git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-11 12:03 -0400 (Thu, 11 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4539 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4474 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
| 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 1149/2322 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.23.0 (landing page) Lauren McIver
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.23.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz |
| StartedAt: 2025-09-11 02:03:15 -0400 (Thu, 11 Sep 2025) |
| EndedAt: 2025-09-11 02:07:38 -0400 (Thu, 11 Sep 2025) |
| EllapsedTime: 263.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Maaslin2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Maaslin2_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.23.0’
* 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_association_plots: no visible binding for global variable
‘xnames’
Undefined global functions or variables:
xnames
* 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 90.242 0.802 91.067
* 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-3.22-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.
Maaslin2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Maaslin2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.23.0’ ** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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"
2025-09-11 02:05:16.864333 INFO::Writing function arguments to log file
2025-09-11 02:05:16.912032 INFO::Verifying options selected are valid
2025-09-11 02:05:16.945566 INFO::Determining format of input files
2025-09-11 02:05:16.947122 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 02:05:16.952261 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-11 02:05:16.953574 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-11 02:05:16.955986 INFO::Filter data based on min abundance and min prevalence
2025-09-11 02:05:16.956884 INFO::Total samples in data: 1595
2025-09-11 02:05:16.957706 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-11 02:05:16.969241 INFO::Total filtered features: 0
2025-09-11 02:05:16.970468 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-11 02:05:16.977247 INFO::Total filtered features with variance filtering: 0
2025-09-11 02:05:16.978304 INFO::Filtered feature names from variance filtering:
2025-09-11 02:05:16.979186 INFO::Running selected normalization method: TSS
2025-09-11 02:05:18.207938 INFO::Bypass z-score application to metadata
2025-09-11 02:05:18.209268 INFO::Running selected transform method: AST
2025-09-11 02:05:18.229567 INFO::Running selected analysis method: LM
2025-09-11 02:05:18.883693 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-11 02:05:19.373641 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-11 02:05:19.546526 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-11 02:05:19.738408 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-11 02:05:19.899215 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-11 02:05:20.05421 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-11 02:05:20.261665 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-11 02:05:20.452906 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-11 02:05:20.576555 WARNING::Fitting problem for feature 8 a warning was issued
2025-09-11 02:05:20.748291 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-11 02:05:20.888873 WARNING::Fitting problem for feature 9 a warning was issued
2025-09-11 02:05:21.079837 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-11 02:05:21.229368 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-11 02:05:21.434918 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-11 02:05:21.593992 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-11 02:05:21.7133 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-11 02:05:21.884322 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-11 02:05:22.075234 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-11 02:05:22.236986 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-11 02:05:22.388278 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-11 02:05:22.588016 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-11 02:05:22.756547 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-11 02:05:22.891935 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-11 02:05:23.054933 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-11 02:05:23.201507 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-11 02:05:23.346485 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-11 02:05:23.523299 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-11 02:05:23.690132 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-11 02:05:23.852236 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-11 02:05:23.995243 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-11 02:05:24.156144 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-11 02:05:24.337445 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-11 02:05:24.527779 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-11 02:05:24.680158 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-11 02:05:24.842181 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-11 02:05:25.000746 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-11 02:05:25.178265 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-11 02:05:25.323905 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-11 02:05:25.479026 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-11 02:05:25.623542 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-11 02:05:25.785782 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-11 02:05:25.938745 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-11 02:05:26.10241 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-11 02:05:26.266937 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-11 02:05:26.470542 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-11 02:05:26.643975 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-11 02:05:26.789781 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-11 02:05:26.947897 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-11 02:05:27.1098 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-11 02:05:27.28164 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-11 02:05:27.448342 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-11 02:05:27.610004 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-11 02:05:27.755597 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-11 02:05:27.920361 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-11 02:05:28.085744 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-11 02:05:28.234418 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-11 02:05:28.386517 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-11 02:05:28.532106 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-11 02:05:28.677732 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-11 02:05:28.836325 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-11 02:05:28.974422 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-11 02:05:29.128299 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-11 02:05:29.277651 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-11 02:05:29.430809 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-11 02:05:29.576506 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-11 02:05:29.736507 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-11 02:05:29.918682 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-11 02:05:30.061193 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-11 02:05:30.210164 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-11 02:05:30.382743 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-11 02:05:30.607507 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-11 02:05:30.813372 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-11 02:05:30.993635 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-11 02:05:31.15366 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-11 02:05:31.298474 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-11 02:05:31.444191 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-11 02:05:31.597995 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-11 02:05:31.749754 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-11 02:05:31.906693 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-11 02:05:32.069092 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-11 02:05:32.225431 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-11 02:05:32.391336 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-11 02:05:32.563129 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-11 02:05:32.711259 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-11 02:05:32.87312 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-11 02:05:33.028533 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-11 02:05:33.170879 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-11 02:05:33.337356 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-11 02:05:33.522087 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-11 02:05:33.699787 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-11 02:05:33.94259 INFO::Counting total values for each feature
2025-09-11 02:05:33.978631 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-11 02:05:34.072637 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-11 02:05:34.16907 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-11 02:05:34.271909 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-11 02:05:34.320244 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-11 02:05:34.599949 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-11 02:05:34.606431 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-11 02:05:34.61161 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"
2025-09-11 02:05:34.6239 INFO::Writing function arguments to log file
2025-09-11 02:05:34.629543 INFO::Verifying options selected are valid
2025-09-11 02:05:34.630591 INFO::Determining format of input files
2025-09-11 02:05:34.631844 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-11 02:05:34.636896 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-11 02:05:34.638016 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-09-11 02:05:34.639681 INFO::Filter data based on min abundance and min prevalence
2025-09-11 02:05:34.640557 INFO::Total samples in data: 1595
2025-09-11 02:05:34.641404 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-11 02:05:34.645024 INFO::Total filtered features: 0
2025-09-11 02:05:34.645997 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-11 02:05:34.651893 INFO::Total filtered features with variance filtering: 0
2025-09-11 02:05:34.652883 INFO::Filtered feature names from variance filtering:
2025-09-11 02:05:34.653694 INFO::Running selected normalization method: NONE
2025-09-11 02:05:34.654498 INFO::Bypass z-score application to metadata
2025-09-11 02:05:34.655299 INFO::Running selected transform method: AST
2025-09-11 02:05:34.668902 INFO::Running selected analysis method: LM
2025-09-11 02:05:34.670498 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-11 02:05:34.80966 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-11 02:05:34.99591 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-11 02:05:35.140994 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-11 02:05:35.292075 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-11 02:05:35.446095 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-11 02:05:35.607461 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-11 02:05:35.755383 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-11 02:05:35.900355 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-11 02:05:36.060435 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-11 02:05:36.216798 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-11 02:05:36.341871 WARNING::Fitting problem for feature 11 a warning was issued
2025-09-11 02:05:36.48989 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-11 02:05:36.632484 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-11 02:05:36.777853 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-11 02:05:36.919897 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-11 02:05:37.072274 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-11 02:05:37.184558 WARNING::Fitting problem for feature 16 a warning was issued
2025-09-11 02:05:37.33164 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-11 02:05:37.487348 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-11 02:05:37.625506 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-11 02:05:37.763229 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-11 02:05:37.923221 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-11 02:05:38.075334 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-11 02:05:38.221434 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-11 02:05:38.367542 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-11 02:05:38.514564 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-11 02:05:38.663417 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-11 02:05:38.837014 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-11 02:05:38.991202 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-11 02:05:39.13289 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-11 02:05:39.289076 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-11 02:05:39.431929 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-11 02:05:39.881868 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-11 02:05:40.020502 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-11 02:05:40.163209 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-11 02:05:40.307218 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-11 02:05:40.456414 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-11 02:05:40.597982 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-11 02:05:40.746649 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-11 02:05:40.890503 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-11 02:05:41.039412 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-11 02:05:41.175191 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-11 02:05:41.313178 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-11 02:05:41.465808 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-11 02:05:41.612684 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-11 02:05:41.754776 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-11 02:05:41.89528 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-11 02:05:42.04895 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-11 02:05:42.186835 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-11 02:05:42.335978 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-11 02:05:42.474754 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-11 02:05:42.612496 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-11 02:05:42.753915 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-11 02:05:42.883936 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-11 02:05:43.024104 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-11 02:05:43.162283 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-11 02:05:43.318127 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-11 02:05:43.461549 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-11 02:05:43.625915 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-11 02:05:43.767489 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-11 02:05:43.931734 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-11 02:05:44.074816 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-11 02:05:44.230821 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-11 02:05:44.375319 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-11 02:05:44.524458 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-11 02:05:44.685307 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-11 02:05:44.835048 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-11 02:05:44.980392 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-11 02:05:45.101339 WARNING::Fitting problem for feature 67 a warning was issued
2025-09-11 02:05:45.276485 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-11 02:05:45.42212 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-11 02:05:45.575175 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-11 02:05:45.74636 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-11 02:05:46.169194 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-11 02:05:46.22371 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-11 02:05:46.366117 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-11 02:05:46.529182 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-11 02:05:46.682871 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-11 02:05:46.839137 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-11 02:05:46.974751 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-11 02:05:47.116657 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-11 02:05:47.280287 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-11 02:05:47.430324 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-11 02:05:47.588548 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-11 02:05:47.73781 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-11 02:05:47.902204 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-11 02:05:48.050139 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-11 02:05:48.196731 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-11 02:05:48.347908 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-11 02:05:48.491997 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-11 02:05:48.664379 INFO::Counting total values for each feature
2025-09-11 02:05:48.686508 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-11 02:05:48.789409 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-11 02:05:48.904375 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-11 02:05:49.009195 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-11 02:05:49.072971 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-11 02:05:49.134423 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-11 02:05:49.139675 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-11 02:05:49.143755 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
32.925 0.501 33.427
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 90.242 | 0.802 | 91.067 | |