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This page was generated on 2025-01-23 12:09 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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: 2025-01-20 13:00 -0500 (Mon, 20 Jan 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 -0500 (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 merida1

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: 2025-01-21 05:56:09 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 06:01:55 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 345.8 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 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* 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 179.823  2.794 202.244
* 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-x86_64/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 1.9.16
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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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"
2025-01-21 06:00:36.178997 INFO::Writing function arguments to log file
2025-01-21 06:00:36.277556 INFO::Verifying options selected are valid
2025-01-21 06:00:36.365217 INFO::Determining format of input files
2025-01-21 06:00:36.368569 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 06:00:36.385704 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 06:00:36.389342 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-21 06:00:36.396245 INFO::Filter data based on min abundance and min prevalence
2025-01-21 06:00:36.398909 INFO::Total samples in data: 1595
2025-01-21 06:00:36.401618 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 06:00:36.413762 INFO::Total filtered features: 0
2025-01-21 06:00:36.416868 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 06:00:36.450669 INFO::Total filtered features with variance filtering: 0
2025-01-21 06:00:36.479538 INFO::Filtered feature names from variance filtering:
2025-01-21 06:00:36.481927 INFO::Running selected normalization method: TSS
2025-01-21 06:00:38.995691 INFO::Bypass z-score application to metadata
2025-01-21 06:00:38.998342 INFO::Running selected transform method: AST
2025-01-21 06:00:39.034683 INFO::Running selected analysis method: LM
2025-01-21 06:00:40.213641 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 06:00:40.963021 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 06:00:41.322811 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 06:00:41.669738 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 06:00:42.062278 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 06:00:42.404884 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 06:00:42.75758 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 06:00:43.143748 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 06:00:43.449876 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 06:00:43.759015 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 06:00:44.061519 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 06:00:44.398248 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 06:00:44.735623 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 06:00:45.067236 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 06:00:45.570756 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 06:00:45.952441 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 06:00:46.313053 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 06:00:46.63364 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 06:00:47.000301 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 06:00:47.361495 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 06:00:47.669884 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 06:00:48.006822 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 06:00:48.337917 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 06:00:48.676693 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 06:00:49.014912 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 06:00:49.347974 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 06:00:49.676999 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 06:00:50.298775 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 06:00:50.632899 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 06:00:50.964569 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 06:00:51.305139 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 06:00:51.627898 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 06:00:52.006148 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 06:00:52.325514 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 06:00:52.678049 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 06:00:52.99432 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 06:00:53.325204 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 06:00:53.947812 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 06:00:54.288785 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 06:00:54.604522 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 06:00:54.940324 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 06:00:55.291533 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 06:00:55.60564 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 06:00:55.923303 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 06:00:56.241135 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 06:00:56.549448 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 06:00:56.876964 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 06:00:57.223016 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 06:00:57.554731 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 06:00:57.860547 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 06:00:58.183442 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 06:00:58.494043 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 06:00:58.800549 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 06:00:59.139533 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 06:00:59.465771 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 06:00:59.76609 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 06:01:00.093487 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 06:01:00.440207 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 06:01:00.771286 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 06:01:01.108338 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 06:01:01.423332 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 06:01:01.737877 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 06:01:02.06198 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 06:01:02.381872 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 06:01:02.972724 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 06:01:03.286794 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 06:01:03.596408 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 06:01:03.920081 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 06:01:04.225918 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 06:01:04.543438 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 06:01:04.886974 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 06:01:05.231958 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 06:01:05.549359 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 06:01:05.883246 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 06:01:06.197951 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 06:01:06.525315 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 06:01:06.871969 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 06:01:07.191045 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 06:01:07.520102 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 06:01:07.862162 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 06:01:08.191827 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 06:01:08.518062 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 06:01:08.867346 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 06:01:09.188603 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 06:01:09.506163 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 06:01:09.816086 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 06:01:10.133748 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 06:01:10.474097 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 06:01:10.932311 INFO::Counting total values for each feature
2025-01-21 06:01:11.022876 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-21 06:01:11.329221 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-21 06:01:11.709531 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-21 06:01:12.075815 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-21 06:01:12.168246 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-21 06:01:12.220582 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-21 06:01:12.231843 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-21 06:01:12.247315 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"
2025-01-21 06:01:12.27801 INFO::Writing function arguments to log file
2025-01-21 06:01:12.294784 INFO::Verifying options selected are valid
2025-01-21 06:01:12.297321 INFO::Determining format of input files
2025-01-21 06:01:12.300292 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 06:01:12.312658 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 06:01:12.315506 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-21 06:01:12.319673 INFO::Filter data based on min abundance and min prevalence
2025-01-21 06:01:12.322075 INFO::Total samples in data: 1595
2025-01-21 06:01:12.324281 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 06:01:12.33297 INFO::Total filtered features: 0
2025-01-21 06:01:12.335574 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 06:01:12.353215 INFO::Total filtered features with variance filtering: 0
2025-01-21 06:01:12.355837 INFO::Filtered feature names from variance filtering:
2025-01-21 06:01:12.358233 INFO::Running selected normalization method: NONE
2025-01-21 06:01:12.360502 INFO::Bypass z-score application to metadata
2025-01-21 06:01:12.362842 INFO::Running selected transform method: AST
2025-01-21 06:01:12.392293 INFO::Running selected analysis method: LM
2025-01-21 06:01:12.395679 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 06:01:12.694003 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 06:01:13.006255 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 06:01:13.316721 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 06:01:13.667929 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 06:01:13.964155 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 06:01:14.29867 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 06:01:14.595747 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 06:01:14.88916 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 06:01:15.291545 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 06:01:15.587348 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 06:01:15.884453 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 06:01:16.16682 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 06:01:16.414768 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 06:01:16.745234 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 06:01:17.055447 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 06:01:17.361031 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 06:01:17.651524 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 06:01:17.9411 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 06:01:18.23785 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 06:01:18.519816 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 06:01:18.821385 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 06:01:19.359974 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 06:01:19.64824 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 06:01:19.950296 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 06:01:20.260495 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 06:01:20.57314 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 06:01:20.865041 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 06:01:21.182109 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 06:01:21.472421 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 06:01:21.77861 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 06:01:22.070464 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 06:01:22.379796 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 06:01:22.70902 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 06:01:23.027346 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 06:01:23.356107 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 06:01:23.666205 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 06:01:23.986671 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 06:01:24.293605 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 06:01:24.587563 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 06:01:24.89937 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 06:01:25.237621 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 06:01:25.548293 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 06:01:25.878333 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 06:01:26.183873 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 06:01:26.487547 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 06:01:26.794532 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 06:01:27.108094 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 06:01:27.400768 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 06:01:27.710975 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 06:01:28.010413 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 06:01:28.306189 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 06:01:28.630544 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 06:01:28.920384 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 06:01:29.214286 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 06:01:29.512562 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 06:01:29.789635 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 06:01:30.069448 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 06:01:30.368318 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 06:01:30.677515 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 06:01:30.995567 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 06:01:31.339323 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 06:01:31.747894 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 06:01:32.064147 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 06:01:32.434956 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 06:01:32.737496 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 06:01:33.019245 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 06:01:33.314369 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 06:01:33.57016 WARNING::Fitting problem for feature 67 a warning was issued
2025-01-21 06:01:33.916677 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 06:01:34.208809 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 06:01:34.507422 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 06:01:34.835202 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 06:01:35.132266 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 06:01:35.240744 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-21 06:01:35.566441 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 06:01:35.87301 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 06:01:36.172473 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 06:01:36.492817 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 06:01:36.803503 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 06:01:37.10672 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 06:01:37.430747 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 06:01:37.749282 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 06:01:38.050407 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 06:01:38.362784 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 06:01:38.654308 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 06:01:39.007665 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 06:01:39.314784 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 06:01:39.610028 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 06:01:39.938607 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 06:01:40.322714 INFO::Counting total values for each feature
2025-01-21 06:01:40.400387 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-21 06:01:40.66553 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-21 06:01:40.927991 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-21 06:01:41.269917 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-21 06:01:41.405352 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-21 06:01:41.541832 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-21 06:01:41.553711 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-21 06:01:41.566841 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 
 62.132   1.103  68.257

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2179.823 2.794202.244