Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-03-24 12:10 -0400 (Mon, 24 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4763
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4494
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4521
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4448
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4414
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: 2025-03-20 13:00 -0400 (Thu, 20 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: 2025-03-21 23:19:39 -0400 (Fri, 21 Mar 2025)
EndedAt: 2025-03-21 23:22:30 -0400 (Fri, 21 Mar 2025)
EllapsedTime: 170.2 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 91.253  1.764  93.537
* 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"
2025-03-21 23:21:45.885847 INFO::Writing function arguments to log file
2025-03-21 23:21:45.930435 INFO::Verifying options selected are valid
2025-03-21 23:21:45.975084 INFO::Determining format of input files
2025-03-21 23:21:45.977167 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 23:21:45.983825 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 23:21:45.985424 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-21 23:21:45.987977 INFO::Filter data based on min abundance and min prevalence
2025-03-21 23:21:45.988987 INFO::Total samples in data: 1595
2025-03-21 23:21:45.989835 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 23:21:45.995306 INFO::Total filtered features: 0
2025-03-21 23:21:45.996832 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 23:21:46.014531 INFO::Total filtered features with variance filtering: 0
2025-03-21 23:21:46.016169 INFO::Filtered feature names from variance filtering:
2025-03-21 23:21:46.017105 INFO::Running selected normalization method: TSS
2025-03-21 23:21:47.328741 INFO::Bypass z-score application to metadata
2025-03-21 23:21:47.330715 INFO::Running selected transform method: AST
2025-03-21 23:21:47.350172 INFO::Running selected analysis method: LM
2025-03-21 23:21:47.966341 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 23:21:48.386146 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 23:21:48.589734 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 23:21:48.781668 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 23:21:48.971333 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 23:21:49.146188 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 23:21:49.323466 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 23:21:49.517915 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 23:21:49.696316 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 23:21:49.836787 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-21 23:21:50.023452 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 23:21:50.206983 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 23:21:50.373476 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 23:21:50.531284 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 23:21:50.754712 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 23:21:50.931183 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 23:21:51.110595 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 23:21:51.311789 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 23:21:51.49159 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 23:21:51.665819 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 23:21:51.838582 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 23:21:52.03314 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 23:21:52.217541 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 23:21:52.391226 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 23:21:52.837711 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 23:21:53.011541 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 23:21:53.191874 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 23:21:53.356431 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 23:21:53.545028 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 23:21:53.71936 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 23:21:53.905114 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 23:21:54.084009 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 23:21:54.259785 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 23:21:54.436791 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 23:21:54.634088 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 23:21:54.799764 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 23:21:54.969555 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 23:21:55.147898 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 23:21:55.335686 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 23:21:55.499799 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 23:21:55.665081 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 23:21:55.85667 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 23:21:56.037997 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 23:21:56.231846 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 23:21:56.408838 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 23:21:56.578803 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 23:21:56.756248 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 23:21:57.26239 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 23:21:57.445215 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 23:21:57.624896 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 23:21:57.821229 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 23:21:58.006841 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 23:21:58.180574 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 23:21:58.367932 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 23:21:58.557227 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 23:21:58.730623 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 23:21:58.911368 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 23:21:59.087022 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 23:21:59.255103 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 23:21:59.445009 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 23:21:59.617744 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 23:21:59.780992 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 23:21:59.957911 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 23:22:00.127087 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 23:22:00.29824 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 23:22:00.470932 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 23:22:00.633115 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 23:22:00.804042 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 23:22:00.973633 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 23:22:01.140808 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 23:22:01.322535 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 23:22:01.51065 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 23:22:01.678492 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 23:22:01.853827 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 23:22:02.016594 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 23:22:02.182055 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 23:22:02.370243 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 23:22:02.544434 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 23:22:02.723945 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 23:22:02.902316 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 23:22:03.087487 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 23:22:03.252 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 23:22:03.445838 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 23:22:03.627479 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 23:22:03.819405 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 23:22:03.995356 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 23:22:04.166185 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 23:22:04.355147 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 23:22:04.577314 INFO::Counting total values for each feature
2025-03-21 23:22:04.615977 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-21 23:22:04.764797 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-21 23:22:04.936308 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-21 23:22:05.107224 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-21 23:22:05.190169 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-21 23:22:05.516804 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-21 23:22:05.526413 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-21 23:22:05.535295 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"
2025-03-21 23:22:05.551398 INFO::Writing function arguments to log file
2025-03-21 23:22:05.558554 INFO::Verifying options selected are valid
2025-03-21 23:22:05.559639 INFO::Determining format of input files
2025-03-21 23:22:05.560787 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 23:22:05.566939 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 23:22:05.568534 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-21 23:22:05.570298 INFO::Filter data based on min abundance and min prevalence
2025-03-21 23:22:05.571221 INFO::Total samples in data: 1595
2025-03-21 23:22:05.572029 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 23:22:05.576636 INFO::Total filtered features: 0
2025-03-21 23:22:05.578086 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 23:22:05.586552 INFO::Total filtered features with variance filtering: 0
2025-03-21 23:22:05.587893 INFO::Filtered feature names from variance filtering:
2025-03-21 23:22:05.588768 INFO::Running selected normalization method: NONE
2025-03-21 23:22:05.589582 INFO::Bypass z-score application to metadata
2025-03-21 23:22:05.590419 INFO::Running selected transform method: AST
2025-03-21 23:22:05.607562 INFO::Running selected analysis method: LM
2025-03-21 23:22:05.609474 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 23:22:05.770546 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 23:22:05.942442 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 23:22:06.099249 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 23:22:06.26616 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 23:22:06.436773 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 23:22:06.621295 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 23:22:06.791503 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 23:22:06.961704 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 23:22:07.137717 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 23:22:07.303384 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 23:22:07.444852 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-21 23:22:07.627205 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 23:22:07.794387 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 23:22:07.924287 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-21 23:22:08.096618 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 23:22:08.267916 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 23:22:08.43282 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 23:22:08.594875 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 23:22:08.780849 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 23:22:08.953433 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 23:22:09.112197 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 23:22:09.289705 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 23:22:09.461648 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 23:22:09.632182 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 23:22:09.794949 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 23:22:09.957401 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 23:22:10.124445 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 23:22:10.307743 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 23:22:10.474903 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 23:22:10.628996 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 23:22:10.791442 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 23:22:10.954281 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 23:22:11.121946 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 23:22:11.289786 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 23:22:11.451683 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 23:22:11.62386 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 23:22:11.78759 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 23:22:11.964115 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 23:22:12.135577 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 23:22:12.324195 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 23:22:12.484201 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 23:22:12.655217 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 23:22:12.821563 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 23:22:12.990328 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 23:22:13.155256 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 23:22:13.253645 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 23:22:13.422143 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 23:22:13.563994 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 23:22:13.7128 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 23:22:13.7878 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 23:22:13.894544 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 23:22:13.97359 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 23:22:14.047584 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 23:22:14.147253 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 23:22:14.249536 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 23:22:14.407357 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 23:22:14.583589 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 23:22:14.762959 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 23:22:14.926943 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 23:22:15.090747 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 23:22:15.266272 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 23:22:15.420025 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 23:22:15.580092 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 23:22:15.752204 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 23:22:15.912855 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 23:22:16.072425 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 23:22:16.242183 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 23:22:16.401619 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 23:22:16.565861 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 23:22:16.737655 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 23:22:16.908879 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 23:22:17.083011 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 23:22:17.256227 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 23:22:17.313664 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-21 23:22:17.478624 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 23:22:17.670351 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 23:22:17.843519 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 23:22:18.011023 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 23:22:18.193809 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 23:22:18.360607 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 23:22:18.534125 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 23:22:18.702559 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 23:22:18.873446 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 23:22:19.043702 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 23:22:19.202495 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 23:22:19.367585 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 23:22:19.52501 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 23:22:19.698714 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 23:22:19.867778 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 23:22:20.070064 INFO::Counting total values for each feature
2025-03-21 23:22:20.097423 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-21 23:22:20.243429 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-21 23:22:20.390625 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-21 23:22:20.572784 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-21 23:22:20.68477 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-21 23:22:20.791844 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-21 23:22:20.80172 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-21 23:22:20.809125 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 
 35.050   0.780  36.014

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin291.253 1.76493.537