Lauren McIver
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/Maaslin2 |
| git_branch: RELEASE_3_21 |
| git_last_commit: fcec85e |
| git_last_commit_date: 2025-04-15 11:48:14 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1154/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Maaslin2 1.22.0 (landing page) Lauren McIver
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.22.0 |
| 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_1.22.0.tar.gz |
| StartedAt: 2025-04-21 20:05:24 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:06:24 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 59.7 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.22.0’
* 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 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 30.028 0.611 30.835
* 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-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘Maaslin2’ ... ** this is package ‘Maaslin2’ version ‘1.22.0’ ** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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"
2025-04-21 20:06:09.107781 INFO::Writing function arguments to log file
2025-04-21 20:06:09.12401 INFO::Verifying options selected are valid
2025-04-21 20:06:09.137409 INFO::Determining format of input files
2025-04-21 20:06:09.138101 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 20:06:09.140364 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-21 20:06:09.140841 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-21 20:06:09.141658 INFO::Filter data based on min abundance and min prevalence
2025-04-21 20:06:09.141979 INFO::Total samples in data: 1595
2025-04-21 20:06:09.142259 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-21 20:06:09.147318 INFO::Total filtered features: 0
2025-04-21 20:06:09.14784 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 20:06:09.151206 INFO::Total filtered features with variance filtering: 0
2025-04-21 20:06:09.151628 INFO::Filtered feature names from variance filtering:
2025-04-21 20:06:09.151956 INFO::Running selected normalization method: TSS
2025-04-21 20:06:09.560094 INFO::Bypass z-score application to metadata
2025-04-21 20:06:09.560696 INFO::Running selected transform method: AST
2025-04-21 20:06:09.566969 INFO::Running selected analysis method: LM
2025-04-21 20:06:09.796146 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-21 20:06:09.932061 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-21 20:06:09.987029 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-21 20:06:10.040675 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-21 20:06:10.098942 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-21 20:06:10.153578 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-21 20:06:10.206243 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-21 20:06:10.26263 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-21 20:06:10.315937 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-21 20:06:10.358534 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-21 20:06:10.415398 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-21 20:06:10.47166 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-21 20:06:10.524553 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-21 20:06:10.576346 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-21 20:06:10.649951 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-21 20:06:10.704889 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-21 20:06:10.759825 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-21 20:06:10.816259 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-21 20:06:10.871529 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-21 20:06:10.9265 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-21 20:06:10.976404 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-21 20:06:11.033217 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-21 20:06:11.085906 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-21 20:06:11.137369 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-21 20:06:11.190413 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-21 20:06:11.245268 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-21 20:06:11.298055 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-21 20:06:11.353683 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-21 20:06:11.410683 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-21 20:06:11.464176 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-21 20:06:11.522619 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-21 20:06:11.574726 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-21 20:06:11.632483 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-21 20:06:11.691502 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-21 20:06:11.747643 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-21 20:06:11.802617 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-21 20:06:11.867978 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-21 20:06:11.922455 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-21 20:06:11.979 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-21 20:06:12.033415 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-21 20:06:12.083572 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-21 20:06:12.141381 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-21 20:06:12.194142 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-21 20:06:12.249503 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-21 20:06:12.305545 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-21 20:06:12.358229 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-21 20:06:12.418021 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-21 20:06:12.477316 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-21 20:06:12.539772 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-21 20:06:12.591891 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-21 20:06:12.651366 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-21 20:06:12.707877 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-21 20:06:12.764496 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-21 20:06:12.830621 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-21 20:06:12.887767 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-21 20:06:12.943042 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-21 20:06:13.002209 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-21 20:06:13.060239 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-21 20:06:13.117191 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-21 20:06:13.17453 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-21 20:06:13.234436 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-21 20:06:13.287639 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-21 20:06:13.349827 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-21 20:06:13.409922 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-21 20:06:13.467167 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-21 20:06:13.538978 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-21 20:06:13.592248 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-21 20:06:13.648875 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-21 20:06:13.708471 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-21 20:06:13.762252 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-21 20:06:13.816535 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-21 20:06:13.875376 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-21 20:06:13.925308 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-21 20:06:13.976054 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-21 20:06:14.030867 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-21 20:06:14.083401 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-21 20:06:14.137333 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-21 20:06:14.197977 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-21 20:06:14.256727 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-21 20:06:14.318138 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-21 20:06:14.381741 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-21 20:06:14.435969 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-21 20:06:14.493449 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-21 20:06:14.555158 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-21 20:06:14.604217 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-21 20:06:14.659777 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-21 20:06:14.709423 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-21 20:06:14.760022 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-21 20:06:14.830343 INFO::Counting total values for each feature
2025-04-21 20:06:14.843518 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-21 20:06:14.891514 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-21 20:06:14.947678 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-21 20:06:15.011909 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-21 20:06:15.039188 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-21 20:06:15.053978 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-21 20:06:15.057487 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-21 20:06:15.060433 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"
2025-04-21 20:06:15.065894 INFO::Writing function arguments to log file
2025-04-21 20:06:15.068167 INFO::Verifying options selected are valid
2025-04-21 20:06:15.068504 INFO::Determining format of input files
2025-04-21 20:06:15.068935 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-21 20:06:15.070997 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-21 20:06:15.071377 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-04-21 20:06:15.071958 INFO::Filter data based on min abundance and min prevalence
2025-04-21 20:06:15.072273 INFO::Total samples in data: 1595
2025-04-21 20:06:15.073723 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-21 20:06:15.075258 INFO::Total filtered features: 0
2025-04-21 20:06:15.075617 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-21 20:06:15.078497 INFO::Total filtered features with variance filtering: 0
2025-04-21 20:06:15.078886 INFO::Filtered feature names from variance filtering:
2025-04-21 20:06:15.079167 INFO::Running selected normalization method: NONE
2025-04-21 20:06:15.079431 INFO::Bypass z-score application to metadata
2025-04-21 20:06:15.079697 INFO::Running selected transform method: AST
2025-04-21 20:06:15.088582 INFO::Running selected analysis method: LM
2025-04-21 20:06:15.089425 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-21 20:06:15.141266 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-21 20:06:15.312339 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-21 20:06:15.364005 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-21 20:06:15.417234 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-21 20:06:15.467881 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-21 20:06:15.52471 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-21 20:06:15.574688 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-21 20:06:15.624746 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-21 20:06:15.676888 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-21 20:06:15.733103 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-21 20:06:15.776663 WARNING::Fitting problem for feature 11 a warning was issued
2025-04-21 20:06:15.833675 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-21 20:06:15.888277 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-21 20:06:15.930256 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-21 20:06:15.983714 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-21 20:06:16.035121 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-21 20:06:16.18204 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-21 20:06:16.228923 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-21 20:06:16.284106 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-21 20:06:16.342509 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-21 20:06:16.400288 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-21 20:06:16.453979 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-21 20:06:16.510558 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-21 20:06:16.569112 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-21 20:06:16.617738 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-21 20:06:16.670703 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-21 20:06:16.720481 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-21 20:06:16.773414 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-21 20:06:16.823752 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-21 20:06:16.871159 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-21 20:06:16.920115 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-21 20:06:16.978791 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-21 20:06:17.029254 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-21 20:06:17.080321 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-21 20:06:17.13163 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-21 20:06:17.183837 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-21 20:06:17.236924 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-21 20:06:17.295349 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-21 20:06:17.348304 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-21 20:06:17.400328 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-21 20:06:17.568265 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-21 20:06:17.615809 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-21 20:06:17.664711 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-21 20:06:17.712624 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-21 20:06:17.767269 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-21 20:06:17.81702 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-21 20:06:17.865084 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-21 20:06:17.917965 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-21 20:06:17.991661 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-21 20:06:18.044136 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-21 20:06:18.0952 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-21 20:06:18.14232 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-21 20:06:18.196798 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-21 20:06:18.260961 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-21 20:06:18.311043 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-21 20:06:18.364078 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-21 20:06:18.421587 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-21 20:06:18.479321 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-21 20:06:18.53271 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-21 20:06:18.584053 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-21 20:06:18.638626 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-21 20:06:18.697103 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-21 20:06:18.748392 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-21 20:06:18.800064 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-21 20:06:18.854532 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-21 20:06:18.916828 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-21 20:06:18.968373 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-21 20:06:19.030621 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-21 20:06:19.081952 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-21 20:06:19.137782 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-21 20:06:19.193149 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-21 20:06:19.249695 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-21 20:06:19.30863 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-21 20:06:19.328671 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-21 20:06:19.389564 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-21 20:06:19.445072 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-21 20:06:19.498321 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-21 20:06:19.548388 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-21 20:06:19.609245 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-21 20:06:19.659405 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-21 20:06:19.711719 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-21 20:06:19.767126 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-21 20:06:19.82829 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-21 20:06:19.885195 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-21 20:06:19.94017 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-21 20:06:19.996041 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-21 20:06:20.053629 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-21 20:06:20.105011 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-21 20:06:20.160887 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-21 20:06:20.226146 INFO::Counting total values for each feature
2025-04-21 20:06:20.236826 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-21 20:06:20.284967 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-21 20:06:20.333025 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-21 20:06:20.400509 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-21 20:06:20.440477 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-21 20:06:20.475594 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-21 20:06:20.478789 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-21 20:06:20.481146 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
11.382 0.378 11.837
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 30.028 | 0.611 | 30.835 | |