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This page was generated on 2025-04-02 19:34 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 kjohnson1

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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2025-04-01 23:23:40 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 23:26:29 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 169.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 90.713  1.734  92.836
* 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-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.15
Current TMB package version is 1.9.17
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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"
2025-04-01 23:25:45.712697 INFO::Writing function arguments to log file
2025-04-01 23:25:45.759863 INFO::Verifying options selected are valid
2025-04-01 23:25:45.797898 INFO::Determining format of input files
2025-04-01 23:25:45.799783 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 23:25:45.805895 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 23:25:45.80735 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-01 23:25:45.80988 INFO::Filter data based on min abundance and min prevalence
2025-04-01 23:25:45.810795 INFO::Total samples in data: 1595
2025-04-01 23:25:45.811624 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 23:25:45.816985 INFO::Total filtered features: 0
2025-04-01 23:25:45.818634 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 23:25:45.83623 INFO::Total filtered features with variance filtering: 0
2025-04-01 23:25:45.837829 INFO::Filtered feature names from variance filtering:
2025-04-01 23:25:45.83879 INFO::Running selected normalization method: TSS
2025-04-01 23:25:47.106872 INFO::Bypass z-score application to metadata
2025-04-01 23:25:47.108723 INFO::Running selected transform method: AST
2025-04-01 23:25:47.12692 INFO::Running selected analysis method: LM
2025-04-01 23:25:47.756294 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 23:25:48.161667 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 23:25:48.336854 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 23:25:48.511877 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 23:25:48.69472 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 23:25:48.857748 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 23:25:49.033722 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 23:25:49.215131 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 23:25:49.395212 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 23:25:49.534676 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-01 23:25:49.717362 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 23:25:49.902811 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 23:25:50.077665 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 23:25:50.25009 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 23:25:50.467206 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 23:25:50.632617 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 23:25:50.805189 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 23:25:51.001003 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 23:25:51.178417 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 23:25:51.354046 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 23:25:51.524511 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 23:25:51.714455 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 23:25:51.889145 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 23:25:52.059626 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 23:25:52.508459 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 23:25:52.684075 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 23:25:52.862193 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 23:25:53.028162 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 23:25:53.220396 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 23:25:53.396552 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 23:25:53.575304 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 23:25:53.752103 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 23:25:53.936908 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 23:25:54.114765 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 23:25:54.314299 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 23:25:54.490757 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 23:25:54.668077 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 23:25:54.84236 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 23:25:55.034861 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 23:25:55.207586 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 23:25:55.379407 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 23:25:55.573988 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 23:25:55.760489 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 23:25:55.943467 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 23:25:56.129476 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 23:25:56.29366 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 23:25:56.465741 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 23:25:56.940317 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 23:25:57.123927 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 23:25:57.301557 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 23:25:57.488767 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 23:25:57.653019 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 23:25:57.818094 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 23:25:58.002013 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 23:25:58.178485 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 23:25:58.340117 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 23:25:58.530269 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 23:25:58.715052 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 23:25:58.879939 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 23:25:59.071785 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 23:25:59.240938 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 23:25:59.41777 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 23:25:59.599816 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 23:25:59.771476 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 23:25:59.944244 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 23:26:00.120864 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 23:26:00.283148 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 23:26:00.450359 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 23:26:00.620405 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 23:26:00.7917 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 23:26:00.981473 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 23:26:01.168562 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 23:26:01.332521 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 23:26:01.508372 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 23:26:01.673396 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 23:26:01.836852 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 23:26:02.013299 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 23:26:02.186031 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 23:26:02.366115 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 23:26:02.546951 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 23:26:02.735012 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 23:26:02.903164 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 23:26:03.098539 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 23:26:03.270911 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 23:26:03.457721 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 23:26:03.626106 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 23:26:03.792819 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 23:26:03.990938 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 23:26:04.208412 INFO::Counting total values for each feature
2025-04-01 23:26:04.248504 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-01 23:26:04.3951 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-01 23:26:04.559252 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-01 23:26:04.729172 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-01 23:26:04.81088 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-01 23:26:05.181162 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-01 23:26:05.19107 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-01 23:26:05.20063 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"
2025-04-01 23:26:05.216312 INFO::Writing function arguments to log file
2025-04-01 23:26:05.222657 INFO::Verifying options selected are valid
2025-04-01 23:26:05.223667 INFO::Determining format of input files
2025-04-01 23:26:05.224767 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 23:26:05.232181 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 23:26:05.233618 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-01 23:26:05.235373 INFO::Filter data based on min abundance and min prevalence
2025-04-01 23:26:05.236266 INFO::Total samples in data: 1595
2025-04-01 23:26:05.237084 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 23:26:05.241668 INFO::Total filtered features: 0
2025-04-01 23:26:05.242932 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 23:26:05.251654 INFO::Total filtered features with variance filtering: 0
2025-04-01 23:26:05.253005 INFO::Filtered feature names from variance filtering:
2025-04-01 23:26:05.253845 INFO::Running selected normalization method: NONE
2025-04-01 23:26:05.254632 INFO::Bypass z-score application to metadata
2025-04-01 23:26:05.2554 INFO::Running selected transform method: AST
2025-04-01 23:26:05.27356 INFO::Running selected analysis method: LM
2025-04-01 23:26:05.275579 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 23:26:05.440165 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 23:26:05.618712 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 23:26:05.779596 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 23:26:05.951352 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 23:26:06.121913 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 23:26:06.301554 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 23:26:06.460559 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 23:26:06.619998 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 23:26:06.792958 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 23:26:06.955155 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 23:26:07.090787 WARNING::Fitting problem for feature 11 a warning was issued
2025-04-01 23:26:07.272394 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 23:26:07.447335 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 23:26:07.585985 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-01 23:26:07.76498 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 23:26:07.947071 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 23:26:08.121272 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 23:26:08.291654 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 23:26:08.481321 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 23:26:08.658749 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 23:26:08.817653 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 23:26:08.991628 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 23:26:09.158514 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 23:26:09.326888 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 23:26:09.498328 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 23:26:09.666822 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 23:26:09.832376 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 23:26:10.005265 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 23:26:10.17107 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 23:26:10.327569 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 23:26:10.491682 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 23:26:10.654369 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 23:26:10.842692 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 23:26:11.009123 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 23:26:11.17327 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 23:26:11.35886 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 23:26:11.532942 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 23:26:11.715241 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 23:26:11.880926 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 23:26:12.052198 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 23:26:12.187982 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 23:26:12.306178 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 23:26:12.418319 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 23:26:12.55453 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 23:26:12.683279 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 23:26:12.784313 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 23:26:12.860939 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 23:26:13.269655 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 23:26:13.426522 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 23:26:13.589316 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 23:26:13.75081 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 23:26:13.912169 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 23:26:14.078428 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 23:26:14.229802 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 23:26:14.395659 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 23:26:14.551584 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 23:26:14.715482 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 23:26:14.882982 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 23:26:15.069426 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 23:26:15.229584 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 23:26:15.399013 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 23:26:15.563308 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 23:26:15.732922 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 23:26:15.887928 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 23:26:16.047852 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 23:26:16.218401 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 23:26:16.380129 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 23:26:16.537032 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 23:26:16.703671 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 23:26:16.876519 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 23:26:17.04439 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 23:26:17.217835 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 23:26:17.393369 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 23:26:17.456305 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-01 23:26:17.622821 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 23:26:17.792704 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 23:26:17.967047 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 23:26:18.131049 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 23:26:18.300705 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 23:26:18.474361 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 23:26:18.627898 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 23:26:18.801045 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 23:26:18.970044 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 23:26:19.141514 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 23:26:19.302687 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 23:26:19.477353 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 23:26:19.641075 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 23:26:19.805939 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 23:26:19.996083 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 23:26:20.184905 INFO::Counting total values for each feature
2025-04-01 23:26:20.22075 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-01 23:26:20.366579 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-01 23:26:20.511593 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-01 23:26:20.683222 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-01 23:26:20.793371 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-01 23:26:20.898449 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-01 23:26:20.907805 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-01 23:26:20.914638 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 
 35.612   0.809  36.549

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin290.713 1.73492.836