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This page was generated on 2025-08-12 12:07 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1146/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.23.0  (landing page)
Lauren McIver
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 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)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Maaslin2 on palomino8

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.

raw results


Summary

Package: Maaslin2
Version: 1.23.0
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Maaslin2_1.23.0.tar.gz
StartedAt: 2025-08-12 03:43:57 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 03:47:31 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 214.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Maaslin2_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 114.61   7.51   123.2
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.


Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2025-08-12 03:46:43.547496 INFO::Writing function arguments to log file
2025-08-12 03:46:43.587568 INFO::Verifying options selected are valid
2025-08-12 03:46:43.622267 INFO::Determining format of input files
2025-08-12 03:46:43.624645 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-12 03:46:43.63986 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-12 03:46:43.642518 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-08-12 03:46:43.646145 INFO::Filter data based on min abundance and min prevalence
2025-08-12 03:46:43.648007 INFO::Total samples in data: 1595
2025-08-12 03:46:43.649856 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-12 03:46:43.655369 INFO::Total filtered features: 0
2025-08-12 03:46:43.657473 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-12 03:46:43.666185 INFO::Total filtered features with variance filtering: 0
2025-08-12 03:46:43.668207 INFO::Filtered feature names from variance filtering:
2025-08-12 03:46:43.669879 INFO::Running selected normalization method: TSS
2025-08-12 03:46:45.026645 INFO::Bypass z-score application to metadata
2025-08-12 03:46:45.029796 INFO::Running selected transform method: AST
2025-08-12 03:46:45.058439 INFO::Running selected analysis method: LM
2025-08-12 03:46:45.720983 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-12 03:46:46.310973 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-12 03:46:46.537041 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-12 03:46:46.765378 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-12 03:46:46.991843 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-12 03:46:47.214268 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-12 03:46:47.447586 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-12 03:46:47.668225 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-12 03:46:47.863309 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-12 03:46:48.084618 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-12 03:46:48.247771 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-12 03:46:48.403744 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-12 03:46:48.542441 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-12 03:46:48.697739 WARNING::Fitting problem for feature 13 a warning was issued
2025-08-12 03:46:48.892754 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-12 03:46:49.078943 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-12 03:46:49.251337 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-12 03:46:49.441851 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-12 03:46:49.654718 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-12 03:46:49.870292 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-12 03:46:50.088598 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-12 03:46:50.303209 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-12 03:46:50.495223 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-12 03:46:50.656485 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-12 03:46:50.831134 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-12 03:46:51.048072 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-12 03:46:51.221417 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-12 03:46:51.405627 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-12 03:46:51.594331 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-12 03:46:51.772982 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-12 03:46:51.949514 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-12 03:46:52.07918 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-12 03:46:52.316636 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-12 03:46:52.488283 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-12 03:46:52.704312 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-12 03:46:52.921115 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-12 03:46:53.127724 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-12 03:46:53.269425 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-12 03:46:53.47058 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-12 03:46:53.618627 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-12 03:46:53.757539 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-12 03:46:53.944016 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-12 03:46:54.116108 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-12 03:46:54.342988 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-12 03:46:54.548388 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-12 03:46:55.03522 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-12 03:46:55.208078 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-12 03:46:55.390506 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-12 03:46:55.590931 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-12 03:46:55.813175 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-12 03:46:56.021811 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-12 03:46:56.22961 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-12 03:46:56.453127 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-12 03:46:56.660467 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-12 03:46:56.899787 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-12 03:46:57.096349 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-12 03:46:57.286632 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-12 03:46:57.507022 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-12 03:46:57.654941 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-12 03:46:57.829637 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-12 03:46:57.998032 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-12 03:46:58.202302 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-12 03:46:58.409378 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-12 03:46:58.603521 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-12 03:46:58.807759 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-12 03:46:58.980163 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-12 03:46:59.167126 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-12 03:46:59.361628 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-12 03:46:59.51507 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-12 03:46:59.718407 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-12 03:46:59.888131 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-12 03:47:00.029853 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-12 03:47:00.235974 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-12 03:47:00.446802 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-12 03:47:00.61776 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-12 03:47:00.756572 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-12 03:47:00.95802 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-12 03:47:01.183538 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-12 03:47:01.368794 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-12 03:47:01.555738 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-12 03:47:01.764885 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-12 03:47:01.958161 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-12 03:47:02.157083 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-12 03:47:02.31669 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-12 03:47:02.521372 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-12 03:47:02.721154 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-12 03:47:02.942019 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-12 03:47:03.134328 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-12 03:47:03.366228 INFO::Counting total values for each feature
2025-08-12 03:47:03.411247 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-08-12 03:47:03.801688 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-08-12 03:47:04.315922 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-08-12 03:47:04.863806 INFO::Writing residuals to file output/fits/residuals.rds
2025-08-12 03:47:04.919541 INFO::Writing fitted values to file output/fits/fitted.rds
2025-08-12 03:47:04.943732 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-08-12 03:47:04.949931 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-08-12 03:47:04.966611 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"
2025-08-12 03:47:05.031057 INFO::Writing function arguments to log file
2025-08-12 03:47:05.045351 INFO::Verifying options selected are valid
2025-08-12 03:47:05.047144 INFO::Determining format of input files
2025-08-12 03:47:05.049292 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-12 03:47:05.058273 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-08-12 03:47:05.061003 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-08-12 03:47:05.064533 INFO::Filter data based on min abundance and min prevalence
2025-08-12 03:47:05.066988 INFO::Total samples in data: 1595
2025-08-12 03:47:05.06946 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-08-12 03:47:05.078129 INFO::Total filtered features: 0
2025-08-12 03:47:05.080927 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-12 03:47:05.094519 INFO::Total filtered features with variance filtering: 0
2025-08-12 03:47:05.098069 INFO::Filtered feature names from variance filtering:
2025-08-12 03:47:05.099907 INFO::Running selected normalization method: NONE
2025-08-12 03:47:05.101621 INFO::Bypass z-score application to metadata
2025-08-12 03:47:05.103318 INFO::Running selected transform method: AST
2025-08-12 03:47:05.126463 INFO::Running selected analysis method: LM
2025-08-12 03:47:05.129487 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-08-12 03:47:05.273202 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-08-12 03:47:05.428419 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-08-12 03:47:05.585211 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-08-12 03:47:05.797748 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-08-12 03:47:05.942062 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-08-12 03:47:06.145604 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-08-12 03:47:06.618547 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-08-12 03:47:06.789556 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-08-12 03:47:06.95759 WARNING::Fitting problem for feature 9 a warning was issued
2025-08-12 03:47:07.132402 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-08-12 03:47:07.294816 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-08-12 03:47:07.40618 WARNING::Fitting problem for feature 11 a warning was issued
2025-08-12 03:47:07.580847 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-08-12 03:47:07.765946 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-08-12 03:47:07.918545 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-08-12 03:47:08.09523 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-08-12 03:47:08.250638 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-08-12 03:47:08.411841 WARNING::Fitting problem for feature 16 a warning was issued
2025-08-12 03:47:08.641699 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-08-12 03:47:08.843191 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-08-12 03:47:09.012952 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-08-12 03:47:09.234072 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-08-12 03:47:09.439144 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-08-12 03:47:09.633623 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-08-12 03:47:09.796221 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-08-12 03:47:09.979106 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-08-12 03:47:10.178231 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-08-12 03:47:10.359559 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-08-12 03:47:10.528378 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-08-12 03:47:10.714596 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-08-12 03:47:10.887191 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-08-12 03:47:11.051489 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-08-12 03:47:11.251629 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-08-12 03:47:11.435826 INFO::Fitting model to feature number 32, Prevotella.copri
2025-08-12 03:47:11.638316 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-08-12 03:47:11.83173 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-08-12 03:47:12.011411 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-08-12 03:47:12.197748 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-08-12 03:47:12.363775 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-08-12 03:47:12.512897 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-08-12 03:47:12.693592 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-08-12 03:47:12.828305 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-08-12 03:47:12.989629 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-08-12 03:47:13.199151 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-08-12 03:47:13.374151 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-08-12 03:47:13.580815 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-08-12 03:47:13.747926 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-08-12 03:47:13.912426 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-08-12 03:47:14.344746 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-08-12 03:47:14.534241 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-08-12 03:47:14.69368 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-08-12 03:47:14.893346 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-08-12 03:47:15.013719 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-08-12 03:47:15.198471 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-08-12 03:47:15.341757 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-08-12 03:47:15.504936 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-08-12 03:47:15.626844 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-08-12 03:47:15.783153 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-08-12 03:47:15.969563 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-08-12 03:47:16.153674 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-08-12 03:47:16.314706 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-08-12 03:47:16.523117 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-08-12 03:47:16.728848 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-08-12 03:47:16.921086 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-08-12 03:47:17.114125 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-08-12 03:47:17.329818 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-08-12 03:47:17.483698 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-08-12 03:47:17.637693 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-08-12 03:47:17.794629 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-08-12 03:47:17.950121 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-08-12 03:47:18.129335 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-08-12 03:47:18.277665 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-08-12 03:47:18.443903 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-08-12 03:47:18.625894 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-08-12 03:47:18.709097 WARNING::Fitting problem for feature 72 a warning was issued
2025-08-12 03:47:18.903331 INFO::Fitting model to feature number 73, Dialister.invisus
2025-08-12 03:47:19.091608 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-08-12 03:47:19.290901 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-08-12 03:47:19.481251 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-08-12 03:47:19.686 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-08-12 03:47:20.08306 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-08-12 03:47:20.28313 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-08-12 03:47:20.436473 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-08-12 03:47:20.637382 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-08-12 03:47:20.777782 INFO::Fitting model to feature number 82, Escherichia.coli
2025-08-12 03:47:20.900438 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-08-12 03:47:21.019955 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-08-12 03:47:21.159725 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-08-12 03:47:21.344087 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-08-12 03:47:21.530726 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-08-12 03:47:21.729792 INFO::Counting total values for each feature
2025-08-12 03:47:21.766681 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-08-12 03:47:22.21613 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-08-12 03:47:22.571469 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-08-12 03:47:23.059753 INFO::Writing residuals to file output2/fits/residuals.rds
2025-08-12 03:47:23.132278 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-08-12 03:47:23.20455 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-08-12 03:47:23.21373 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-08-12 03:47:23.233469 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  40.25    0.92   41.25 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2114.61 7.51123.20