Lauren McIver
| Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 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 2025-09-04 12:05 -0400 (Thu, 04 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1148/2321 | 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: /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_1.23.0.tar.gz |
| StartedAt: 2025-09-03 21:47:13 -0400 (Wed, 03 Sep 2025) |
| EndedAt: 2025-09-03 21:50:13 -0400 (Wed, 03 Sep 2025) |
| EllapsedTime: 180.4 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 97.401 1.786 100.005
* 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-3.22-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-x86_64/Resources/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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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"
2025-09-03 21:49:32.983657 INFO::Writing function arguments to log file
2025-09-03 21:49:33.031554 INFO::Verifying options selected are valid
2025-09-03 21:49:33.070517 INFO::Determining format of input files
2025-09-03 21:49:33.07307 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-03 21:49:33.080847 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-03 21:49:33.082388 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-09-03 21:49:33.085388 INFO::Filter data based on min abundance and min prevalence
2025-09-03 21:49:33.086475 INFO::Total samples in data: 1595
2025-09-03 21:49:33.087485 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-03 21:49:33.100971 INFO::Total filtered features: 0
2025-09-03 21:49:33.102598 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-03 21:49:33.113088 INFO::Total filtered features with variance filtering: 0
2025-09-03 21:49:33.114619 INFO::Filtered feature names from variance filtering:
2025-09-03 21:49:33.116233 INFO::Running selected normalization method: TSS
2025-09-03 21:49:34.345825 INFO::Bypass z-score application to metadata
2025-09-03 21:49:34.347745 INFO::Running selected transform method: AST
2025-09-03 21:49:34.365776 INFO::Running selected analysis method: LM
2025-09-03 21:49:35.06165 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-03 21:49:35.645063 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-03 21:49:35.804192 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-03 21:49:35.99748 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-03 21:49:36.175633 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-03 21:49:36.331804 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-03 21:49:36.49356 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-03 21:49:36.669376 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-03 21:49:36.828576 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-03 21:49:36.989102 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-03 21:49:37.150207 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-03 21:49:37.311796 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-03 21:49:37.45869 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-03 21:49:37.626052 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-03 21:49:37.799469 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-03 21:49:37.965819 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-03 21:49:38.137387 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-03 21:49:38.300569 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-03 21:49:38.463349 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-03 21:49:38.624095 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-03 21:49:38.793747 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-03 21:49:38.956204 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-03 21:49:39.115657 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-03 21:49:39.286387 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-03 21:49:39.442279 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-03 21:49:39.60616 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-03 21:49:39.776239 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-03 21:49:39.938513 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-03 21:49:40.115367 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-03 21:49:40.301222 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-03 21:49:40.472177 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-03 21:49:40.637307 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-03 21:49:40.821447 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-03 21:49:40.994205 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-03 21:49:41.159975 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-03 21:49:41.322472 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-03 21:49:41.481134 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-03 21:49:41.655272 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-03 21:49:41.827481 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-03 21:49:41.979679 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-03 21:49:42.153124 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-03 21:49:42.321794 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-03 21:49:42.514926 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-03 21:49:42.681668 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-03 21:49:42.830357 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-03 21:49:42.994293 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-03 21:49:43.168996 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-03 21:49:43.330522 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-03 21:49:43.49194 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-03 21:49:43.657935 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-03 21:49:43.800169 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-03 21:49:43.964566 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-03 21:49:44.148332 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-03 21:49:44.306584 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-03 21:49:44.459815 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-03 21:49:44.611163 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-03 21:49:44.764971 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-03 21:49:44.945618 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-03 21:49:45.098801 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-03 21:49:45.251208 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-03 21:49:45.397392 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-03 21:49:45.558645 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-03 21:49:45.719279 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-03 21:49:45.886955 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-03 21:49:46.050334 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-03 21:49:46.199091 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-03 21:49:46.360765 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-03 21:49:46.515795 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-03 21:49:46.671198 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-03 21:49:46.827536 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-03 21:49:46.987769 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-03 21:49:47.167353 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-03 21:49:47.308396 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-03 21:49:47.465917 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-03 21:49:47.629738 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-03 21:49:48.035699 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-03 21:49:48.184582 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-03 21:49:48.340251 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-03 21:49:48.475661 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-03 21:49:48.653931 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-03 21:49:48.800004 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-03 21:49:48.941469 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-03 21:49:49.107933 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-03 21:49:49.29669 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-03 21:49:49.457893 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-03 21:49:49.604762 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-03 21:49:49.759833 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-03 21:49:49.920044 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-03 21:49:50.110375 INFO::Counting total values for each feature
2025-09-03 21:49:50.144989 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-09-03 21:49:50.27234 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-09-03 21:49:50.42512 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-09-03 21:49:50.584431 INFO::Writing residuals to file output/fits/residuals.rds
2025-09-03 21:49:50.647153 INFO::Writing fitted values to file output/fits/fitted.rds
2025-09-03 21:49:50.681803 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-09-03 21:49:50.689332 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-09-03 21:49:50.696638 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"
2025-09-03 21:49:50.713431 INFO::Writing function arguments to log file
2025-09-03 21:49:50.722742 INFO::Verifying options selected are valid
2025-09-03 21:49:50.724488 INFO::Determining format of input files
2025-09-03 21:49:50.726236 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-03 21:49:50.734332 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-09-03 21:49:50.736243 INFO::Formula for fixed effects: expr ~ diagnosis + dysbiosis + antibiotics + age
2025-09-03 21:49:50.738832 INFO::Filter data based on min abundance and min prevalence
2025-09-03 21:49:50.740347 INFO::Total samples in data: 1595
2025-09-03 21:49:50.74178 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-09-03 21:49:50.747133 INFO::Total filtered features: 0
2025-09-03 21:49:50.748942 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-03 21:49:50.75866 INFO::Total filtered features with variance filtering: 0
2025-09-03 21:49:50.760779 INFO::Filtered feature names from variance filtering:
2025-09-03 21:49:50.762347 INFO::Running selected normalization method: NONE
2025-09-03 21:49:50.763788 INFO::Bypass z-score application to metadata
2025-09-03 21:49:50.765154 INFO::Running selected transform method: AST
2025-09-03 21:49:50.797052 INFO::Running selected analysis method: LM
2025-09-03 21:49:50.799049 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-09-03 21:49:50.943957 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-09-03 21:49:51.100973 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-09-03 21:49:51.254902 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-09-03 21:49:51.430999 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-09-03 21:49:51.571536 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-09-03 21:49:51.721835 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-09-03 21:49:51.866399 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-09-03 21:49:52.018499 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-09-03 21:49:52.164787 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-09-03 21:49:52.314459 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-09-03 21:49:52.488187 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-09-03 21:49:52.637822 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-09-03 21:49:52.764246 WARNING::Fitting problem for feature 13 a warning was issued
2025-09-03 21:49:52.927547 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-09-03 21:49:53.082366 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-09-03 21:49:53.243564 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-09-03 21:49:53.38898 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-09-03 21:49:53.555071 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-09-03 21:49:53.708741 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-09-03 21:49:53.867011 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-09-03 21:49:54.022455 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-09-03 21:49:54.197951 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-09-03 21:49:54.354971 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-09-03 21:49:54.491576 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-09-03 21:49:54.658963 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-09-03 21:49:54.809422 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-09-03 21:49:54.969364 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-09-03 21:49:55.139398 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-09-03 21:49:55.28612 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-09-03 21:49:55.435229 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-09-03 21:49:55.605825 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-09-03 21:49:55.754044 INFO::Fitting model to feature number 32, Prevotella.copri
2025-09-03 21:49:55.919968 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-09-03 21:49:56.079816 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-09-03 21:49:56.240817 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-09-03 21:49:56.403125 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-09-03 21:49:56.571929 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-09-03 21:49:56.730149 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-09-03 21:49:56.900292 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-09-03 21:49:57.051825 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-09-03 21:49:57.206577 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-09-03 21:49:57.36891 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-09-03 21:49:57.527816 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-09-03 21:49:57.68494 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-09-03 21:49:57.84706 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-09-03 21:49:58.000857 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-09-03 21:49:58.166379 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-09-03 21:49:58.310824 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-09-03 21:49:58.481877 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-09-03 21:49:58.624744 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-09-03 21:49:58.78883 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-09-03 21:49:58.942077 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-09-03 21:49:59.097412 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-09-03 21:49:59.225959 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-09-03 21:49:59.394995 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-09-03 21:49:59.536725 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-09-03 21:49:59.70425 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-09-03 21:49:59.870452 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-09-03 21:50:00.035673 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-09-03 21:50:00.182789 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-09-03 21:50:00.322003 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-09-03 21:50:00.458763 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-09-03 21:50:00.610165 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-09-03 21:50:00.788846 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-09-03 21:50:00.944317 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-09-03 21:50:01.100748 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-09-03 21:50:01.25909 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-09-03 21:50:01.402053 WARNING::Fitting problem for feature 67 a warning was issued
2025-09-03 21:50:01.564953 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-09-03 21:50:01.715609 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-09-03 21:50:01.874347 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-09-03 21:50:02.028568 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-09-03 21:50:02.17751 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-09-03 21:50:02.23067 WARNING::Fitting problem for feature 72 a warning was issued
2025-09-03 21:50:02.393597 INFO::Fitting model to feature number 73, Dialister.invisus
2025-09-03 21:50:02.562211 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-09-03 21:50:02.713729 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-09-03 21:50:02.869734 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-09-03 21:50:03.028068 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-09-03 21:50:03.175192 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-09-03 21:50:03.308461 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-09-03 21:50:03.468129 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-09-03 21:50:03.594357 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-09-03 21:50:03.762383 INFO::Fitting model to feature number 82, Escherichia.coli
2025-09-03 21:50:03.908375 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-09-03 21:50:04.055381 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-09-03 21:50:04.204161 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-09-03 21:50:04.353611 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-09-03 21:50:04.517783 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-09-03 21:50:04.702011 INFO::Counting total values for each feature
2025-09-03 21:50:04.726503 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-09-03 21:50:04.863039 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-09-03 21:50:04.98096 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-09-03 21:50:05.138346 INFO::Writing residuals to file output2/fits/residuals.rds
2025-09-03 21:50:05.21632 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-09-03 21:50:05.28745 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-09-03 21:50:05.294354 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-09-03 21:50:05.300452 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
32.837 0.713 33.745
Maaslin2.Rcheck/Maaslin2-Ex.timings
| name | user | system | elapsed | |
| Maaslin2 | 97.401 | 1.786 | 100.005 | |