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This page was generated on 2024-03-29 11:36:05 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 1124/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.16.0  (landing page)
Lauren McIver
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_18
git_last_commit: 0ab531d
git_last_commit_date: 2023-10-24 11:15:22 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for Maaslin2 on nebbiolo2


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: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Maaslin2_1.16.0.tar.gz
StartedAt: 2024-03-27 23:49:20 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:53:24 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 243.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Maaslin2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.16.0’
* 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 R 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 loading without being on the library search path ... 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 84.866  0.652  85.455
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘maaslin2.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** 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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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"
2024-03-27 23:51:13.889933 INFO::Writing function arguments to log file
2024-03-27 23:51:13.930229 INFO::Verifying options selected are valid
2024-03-27 23:51:13.96711 INFO::Determining format of input files
2024-03-27 23:51:13.968689 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-27 23:51:13.973829 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-27 23:51:13.975229 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-03-27 23:51:13.977621 INFO::Filter data based on min abundance and min prevalence
2024-03-27 23:51:13.978579 INFO::Total samples in data: 1595
2024-03-27 23:51:13.979421 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-27 23:51:13.98333 INFO::Total filtered features: 0
2024-03-27 23:51:13.984495 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-27 23:51:13.991745 INFO::Total filtered features with variance filtering: 0
2024-03-27 23:51:13.992967 INFO::Filtered feature names from variance filtering:
2024-03-27 23:51:13.993915 INFO::Running selected normalization method: TSS
2024-03-27 23:51:15.173403 INFO::Bypass z-score application to metadata
2024-03-27 23:51:15.174624 INFO::Running selected transform method: AST
2024-03-27 23:51:15.190123 INFO::Running selected analysis method: LM
2024-03-27 23:51:15.755652 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-27 23:51:16.106732 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-27 23:51:16.28269 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-27 23:51:16.423929 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-27 23:51:16.572446 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-27 23:51:16.715979 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-27 23:51:16.865109 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-27 23:51:17.004361 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-27 23:51:17.119971 WARNING::Fitting problem for feature 8 a warning was issued
2024-03-27 23:51:17.297607 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-27 23:51:17.408423 WARNING::Fitting problem for feature 9 a warning was issued
2024-03-27 23:51:17.559923 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-27 23:51:17.695662 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-27 23:51:17.843063 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-27 23:51:17.979095 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-27 23:51:18.09451 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-27 23:51:18.24754 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-27 23:51:18.38546 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-27 23:51:18.525446 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-27 23:51:18.660284 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-27 23:51:18.807459 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-27 23:51:18.957328 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-27 23:51:19.104356 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-27 23:51:19.265954 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-27 23:51:19.41404 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-27 23:51:19.552682 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-27 23:51:19.692697 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-27 23:51:19.834654 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-27 23:51:19.974698 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-27 23:51:20.115511 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-27 23:51:20.262153 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-27 23:51:20.412663 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-27 23:51:20.56562 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-27 23:51:20.70265 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-27 23:51:20.850356 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-27 23:51:20.999952 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-27 23:51:21.154015 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-27 23:51:21.309028 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-27 23:51:21.45443 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-27 23:51:21.602525 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-27 23:51:21.755393 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-27 23:51:21.888453 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-27 23:51:22.056893 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-27 23:51:22.199943 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-27 23:51:22.342546 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-27 23:51:22.490934 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-27 23:51:22.635328 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-27 23:51:22.768091 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-27 23:51:22.906133 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-27 23:51:23.053219 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-27 23:51:23.203789 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-27 23:51:23.351614 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-27 23:51:23.501925 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-27 23:51:23.644937 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-27 23:51:23.803792 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-27 23:51:23.970526 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-27 23:51:24.126083 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-27 23:51:24.262594 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-27 23:51:24.41079 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-27 23:51:24.555717 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-27 23:51:24.690717 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-27 23:51:24.839418 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-27 23:51:24.97717 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-27 23:51:25.117447 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-27 23:51:25.259353 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-27 23:51:25.399608 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-27 23:51:25.546163 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-27 23:51:25.680197 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-27 23:51:25.818462 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-27 23:51:25.960193 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-27 23:51:26.090876 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-27 23:51:26.236477 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-27 23:51:26.386428 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-27 23:51:26.793475 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-27 23:51:26.930502 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-27 23:51:27.075372 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-27 23:51:27.224905 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-27 23:51:27.369418 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-27 23:51:27.51161 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-27 23:51:27.653733 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-27 23:51:27.805985 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-27 23:51:27.961096 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-27 23:51:28.110969 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-27 23:51:28.258599 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-27 23:51:28.407514 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-27 23:51:28.54784 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-27 23:51:28.688744 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-27 23:51:28.826216 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-27 23:51:28.961077 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-27 23:51:29.101308 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-27 23:51:29.281305 INFO::Counting total values for each feature
2024-03-27 23:51:29.32277 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-03-27 23:51:29.46705 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-03-27 23:51:29.615555 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-03-27 23:51:29.766024 INFO::Writing residuals to file output/fits/residuals.rds
2024-03-27 23:51:29.82847 INFO::Writing fitted values to file output/fits/fitted.rds
2024-03-27 23:51:29.860876 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-03-27 23:51:29.866822 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-03-27 23:51:29.874426 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"
2024-03-27 23:51:29.891157 INFO::Writing function arguments to log file
2024-03-27 23:51:29.897187 INFO::Verifying options selected are valid
2024-03-27 23:51:29.898343 INFO::Determining format of input files
2024-03-27 23:51:29.899593 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-27 23:51:29.905207 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-27 23:51:29.906373 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-03-27 23:51:29.908078 INFO::Filter data based on min abundance and min prevalence
2024-03-27 23:51:29.908918 INFO::Total samples in data: 1595
2024-03-27 23:51:29.909724 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-27 23:51:29.913968 INFO::Total filtered features: 0
2024-03-27 23:51:29.914901 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-27 23:51:29.922922 INFO::Total filtered features with variance filtering: 0
2024-03-27 23:51:29.924152 INFO::Filtered feature names from variance filtering:
2024-03-27 23:51:29.925061 INFO::Running selected normalization method: NONE
2024-03-27 23:51:29.925905 INFO::Bypass z-score application to metadata
2024-03-27 23:51:29.926778 INFO::Running selected transform method: AST
2024-03-27 23:51:29.957729 INFO::Running selected analysis method: LM
2024-03-27 23:51:29.959801 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-27 23:51:30.103898 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-27 23:51:30.24805 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-27 23:51:30.376429 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-27 23:51:30.516398 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-27 23:51:30.64544 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-27 23:51:30.788001 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-27 23:51:30.920549 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-27 23:51:31.05685 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-27 23:51:31.21157 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-27 23:51:31.353942 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-27 23:51:31.475418 WARNING::Fitting problem for feature 11 a warning was issued
2024-03-27 23:51:31.63126 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-27 23:51:31.763239 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-27 23:51:31.901754 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-27 23:51:32.046799 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-27 23:51:32.188664 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-27 23:51:32.296083 WARNING::Fitting problem for feature 16 a warning was issued
2024-03-27 23:51:32.448393 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-27 23:51:32.590755 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-27 23:51:32.729015 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-27 23:51:32.874804 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-27 23:51:33.012233 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-27 23:51:33.158231 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-27 23:51:33.299826 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-27 23:51:33.436573 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-27 23:51:33.584073 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-27 23:51:33.721311 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-27 23:51:33.861004 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-27 23:51:33.997898 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-27 23:51:34.134931 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-27 23:51:34.263131 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-27 23:51:34.402331 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-27 23:51:34.534352 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-27 23:51:34.676898 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-27 23:51:34.805171 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-27 23:51:34.936283 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-27 23:51:35.313684 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-27 23:51:35.445208 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-27 23:51:35.577432 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-27 23:51:35.714375 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-27 23:51:35.851394 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-27 23:51:35.979836 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-27 23:51:36.116349 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-27 23:51:36.250677 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-27 23:51:36.391538 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-27 23:51:36.52689 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-27 23:51:36.658061 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-27 23:51:36.800777 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-27 23:51:36.927296 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-27 23:51:37.061107 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-27 23:51:37.195086 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-27 23:51:37.327394 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-27 23:51:37.463008 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-27 23:51:37.585349 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-27 23:51:37.970457 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-27 23:51:38.099644 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-27 23:51:38.231876 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-27 23:51:38.366593 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-27 23:51:38.505738 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-27 23:51:38.645567 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-27 23:51:38.776245 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-27 23:51:38.901835 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-27 23:51:39.032234 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-27 23:51:39.164443 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-27 23:51:39.311572 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-27 23:51:39.442679 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-27 23:51:39.572953 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-27 23:51:39.702495 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-27 23:51:39.813758 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-27 23:51:39.96256 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-27 23:51:40.089404 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-27 23:51:40.227583 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-27 23:51:40.368182 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-27 23:51:40.50115 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-27 23:51:40.55976 WARNING::Fitting problem for feature 72 a warning was issued
2024-03-27 23:51:40.692864 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-27 23:51:40.823943 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-27 23:51:40.958512 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-27 23:51:41.090813 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-27 23:51:41.231884 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-27 23:51:41.362645 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-27 23:51:41.49545 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-27 23:51:41.633914 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-27 23:51:41.767997 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-27 23:51:41.909868 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-27 23:51:42.040512 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-27 23:51:42.168253 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-27 23:51:42.299529 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-27 23:51:42.441058 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-27 23:51:42.593431 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-27 23:51:42.751016 INFO::Counting total values for each feature
2024-03-27 23:51:42.773884 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-03-27 23:51:42.916288 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-03-27 23:51:43.075022 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-03-27 23:51:43.225632 INFO::Writing residuals to file output2/fits/residuals.rds
2024-03-27 23:51:43.299973 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-03-27 23:51:43.371178 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-03-27 23:51:43.376709 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-03-27 23:51:43.381857 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.099   0.510  30.597

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin284.866 0.65285.455