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This page was generated on 2024-05-18 11:37:58 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 1138/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.18.0  (landing page)
Lauren McIver
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for Maaslin2 on lconway


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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-05-17 21:52:52 -0400 (Fri, 17 May 2024)
EndedAt: 2024-05-17 21:55:59 -0400 (Fri, 17 May 2024)
EllapsedTime: 187.2 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* 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 97.48  2.178 100.593
* 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-3.19-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 checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.10
Current TMB version is 1.9.11
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 4.4.0 (2024-04-24) -- "Puppy Cup"
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"
2024-05-17 21:55:14.841819 INFO::Writing function arguments to log file
2024-05-17 21:55:14.901799 INFO::Verifying options selected are valid
2024-05-17 21:55:14.944631 INFO::Determining format of input files
2024-05-17 21:55:14.94751 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-17 21:55:14.956133 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-17 21:55:14.958383 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-17 21:55:14.962325 INFO::Filter data based on min abundance and min prevalence
2024-05-17 21:55:14.963945 INFO::Total samples in data: 1595
2024-05-17 21:55:14.965426 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-17 21:55:14.980597 INFO::Total filtered features: 0
2024-05-17 21:55:14.982831 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-17 21:55:14.99533 INFO::Total filtered features with variance filtering: 0
2024-05-17 21:55:14.997263 INFO::Filtered feature names from variance filtering:
2024-05-17 21:55:14.998985 INFO::Running selected normalization method: TSS
2024-05-17 21:55:16.3751 INFO::Bypass z-score application to metadata
2024-05-17 21:55:16.377301 INFO::Running selected transform method: AST
2024-05-17 21:55:16.394616 INFO::Running selected analysis method: LM
2024-05-17 21:55:16.99378 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-17 21:55:17.408037 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-17 21:55:17.608814 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-17 21:55:17.779807 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-17 21:55:17.9704 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-17 21:55:18.13989 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-17 21:55:18.318026 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-17 21:55:18.501162 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-17 21:55:18.68446 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-17 21:55:18.896358 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-17 21:55:19.065702 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-17 21:55:19.25043 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-17 21:55:19.437019 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-17 21:55:19.563025 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-17 21:55:19.755264 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-17 21:55:19.929833 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-17 21:55:20.110051 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-17 21:55:20.274082 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-17 21:55:20.458922 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-17 21:55:20.62263 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-17 21:55:20.788957 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-17 21:55:20.973081 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-17 21:55:21.14739 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-17 21:55:21.331108 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-17 21:55:21.497298 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-17 21:55:21.672822 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-17 21:55:21.845548 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-17 21:55:22.013034 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-17 21:55:22.207964 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-17 21:55:22.377305 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-17 21:55:22.558828 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-17 21:55:22.732593 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-17 21:55:22.911707 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-17 21:55:23.079402 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-17 21:55:23.295116 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-17 21:55:23.463954 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-17 21:55:23.649369 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-17 21:55:23.823714 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-17 21:55:23.972938 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-17 21:55:24.150866 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-17 21:55:24.304333 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-17 21:55:24.48431 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-17 21:55:24.66566 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-17 21:55:24.840988 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-17 21:55:25.007763 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-17 21:55:25.180691 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-17 21:55:25.361281 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-17 21:55:25.527876 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-17 21:55:25.953288 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-17 21:55:26.126526 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-17 21:55:26.303431 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-17 21:55:26.490939 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-17 21:55:26.657755 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-17 21:55:26.825744 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-17 21:55:27.012647 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-17 21:55:27.192736 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-17 21:55:27.363039 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-17 21:55:27.545305 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-17 21:55:27.722341 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-17 21:55:27.897737 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-17 21:55:28.06956 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-17 21:55:28.263156 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-17 21:55:28.431877 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-17 21:55:28.610635 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-17 21:55:28.805761 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-17 21:55:28.97581 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-17 21:55:29.132855 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-17 21:55:29.323886 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-17 21:55:29.495525 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-17 21:55:29.674552 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-17 21:55:29.864418 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-17 21:55:30.045506 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-17 21:55:30.228869 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-17 21:55:30.403308 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-17 21:55:30.571076 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-17 21:55:30.747422 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-17 21:55:30.912292 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-17 21:55:31.084295 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-17 21:55:31.263856 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-17 21:55:31.429839 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-17 21:55:31.608895 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-17 21:55:31.774992 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-17 21:55:32.204106 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-17 21:55:32.384474 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-17 21:55:32.557122 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-17 21:55:32.718038 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-17 21:55:32.898865 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-17 21:55:33.065359 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-17 21:55:33.290009 INFO::Counting total values for each feature
2024-05-17 21:55:33.330374 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-17 21:55:33.466996 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-17 21:55:33.640443 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-17 21:55:33.821439 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-17 21:55:33.882765 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-17 21:55:33.915247 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-17 21:55:33.923753 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-17 21:55:33.932762 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"
2024-05-17 21:55:33.95239 INFO::Writing function arguments to log file
2024-05-17 21:55:33.963177 INFO::Verifying options selected are valid
2024-05-17 21:55:33.964858 INFO::Determining format of input files
2024-05-17 21:55:33.966919 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-17 21:55:33.973233 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-17 21:55:33.974773 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-17 21:55:33.977782 INFO::Filter data based on min abundance and min prevalence
2024-05-17 21:55:33.979349 INFO::Total samples in data: 1595
2024-05-17 21:55:33.98082 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-17 21:55:33.997267 INFO::Total filtered features: 0
2024-05-17 21:55:33.999656 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-17 21:55:34.008203 INFO::Total filtered features with variance filtering: 0
2024-05-17 21:55:34.010528 INFO::Filtered feature names from variance filtering:
2024-05-17 21:55:34.012248 INFO::Running selected normalization method: NONE
2024-05-17 21:55:34.013858 INFO::Bypass z-score application to metadata
2024-05-17 21:55:34.015345 INFO::Running selected transform method: AST
2024-05-17 21:55:34.032792 INFO::Running selected analysis method: LM
2024-05-17 21:55:34.035341 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-17 21:55:34.211336 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-17 21:55:34.377001 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-17 21:55:34.54697 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-17 21:55:34.721066 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-17 21:55:34.886669 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-17 21:55:35.048534 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-17 21:55:35.223192 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-17 21:55:35.40227 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-17 21:55:35.556922 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-17 21:55:35.721888 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-17 21:55:35.899473 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-17 21:55:36.08899 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-17 21:55:36.213881 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-17 21:55:36.385196 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-17 21:55:36.555125 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-17 21:55:36.740419 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-17 21:55:36.910749 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-17 21:55:37.080362 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-17 21:55:37.255639 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-17 21:55:37.428188 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-17 21:55:37.599718 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-17 21:55:37.77124 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-17 21:55:37.953432 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-17 21:55:38.131256 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-17 21:55:38.290336 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-17 21:55:38.451163 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-17 21:55:38.620321 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-17 21:55:38.797117 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-17 21:55:38.940204 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-17 21:55:39.109461 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-17 21:55:39.282371 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-17 21:55:39.461854 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-17 21:55:39.642614 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-17 21:55:39.81717 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-17 21:55:39.992666 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-17 21:55:40.161318 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-17 21:55:40.333694 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-17 21:55:40.491339 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-17 21:55:40.658021 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-17 21:55:40.817103 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-17 21:55:40.976295 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-17 21:55:41.140449 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-17 21:55:41.29814 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-17 21:55:41.454924 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-17 21:55:41.633669 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-17 21:55:41.795111 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-17 21:55:41.954884 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-17 21:55:42.110903 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-17 21:55:42.283962 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-17 21:55:42.430061 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-17 21:55:42.588007 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-17 21:55:42.746977 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-17 21:55:42.922803 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-17 21:55:43.077261 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-17 21:55:43.23413 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-17 21:55:43.403526 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-17 21:55:43.596756 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-17 21:55:43.758805 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-17 21:55:43.920555 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-17 21:55:44.087856 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-17 21:55:44.26138 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-17 21:55:44.432112 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-17 21:55:44.597517 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-17 21:55:44.763382 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-17 21:55:44.944026 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-17 21:55:45.119719 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-17 21:55:45.291134 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-17 21:55:45.424293 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-17 21:55:45.600803 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-17 21:55:45.760148 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-17 21:55:45.930097 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-17 21:55:46.100735 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-17 21:55:46.261685 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-17 21:55:46.32067 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-17 21:55:46.496704 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-17 21:55:46.67894 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-17 21:55:46.819745 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-17 21:55:46.97902 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-17 21:55:47.166097 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-17 21:55:47.353078 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-17 21:55:47.505656 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-17 21:55:47.677795 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-17 21:55:47.861433 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-17 21:55:48.061149 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-17 21:55:48.225208 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-17 21:55:48.649748 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-17 21:55:48.827592 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-17 21:55:48.966746 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-17 21:55:49.125849 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-17 21:55:49.336617 INFO::Counting total values for each feature
2024-05-17 21:55:49.365809 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-17 21:55:49.511372 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-17 21:55:49.639795 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-17 21:55:49.797806 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-17 21:55:49.869126 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-17 21:55:49.939786 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-17 21:55:49.948306 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-17 21:55:49.956619 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 
 35.363   0.928  36.639

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 97.480 2.178100.593