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This page was generated on 2024-07-18 11:40 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 1111/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on palomino8

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: 1.19.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-07-18 02:33:36 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 02:37:03 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 207.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.19.0'
* 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 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 110.6    7.1  117.89
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2024-07-18 02:36:15.501959 INFO::Writing function arguments to log file
2024-07-18 02:36:15.561544 INFO::Verifying options selected are valid
2024-07-18 02:36:15.61321 INFO::Determining format of input files
2024-07-18 02:36:15.616915 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-18 02:36:15.638799 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-18 02:36:15.642527 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-18 02:36:15.648028 INFO::Filter data based on min abundance and min prevalence
2024-07-18 02:36:15.651016 INFO::Total samples in data: 1595
2024-07-18 02:36:15.653956 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-18 02:36:15.662577 INFO::Total filtered features: 0
2024-07-18 02:36:15.665673 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-18 02:36:15.679469 INFO::Total filtered features with variance filtering: 0
2024-07-18 02:36:15.682608 INFO::Filtered feature names from variance filtering:
2024-07-18 02:36:15.685467 INFO::Running selected normalization method: TSS
2024-07-18 02:36:17.062924 INFO::Bypass z-score application to metadata
2024-07-18 02:36:17.066418 INFO::Running selected transform method: AST
2024-07-18 02:36:17.094645 INFO::Running selected analysis method: LM
2024-07-18 02:36:17.50054 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-18 02:36:18.01462 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-18 02:36:18.239002 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-18 02:36:18.457712 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-18 02:36:18.662001 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-18 02:36:18.872079 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-18 02:36:19.078663 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-18 02:36:19.334773 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-18 02:36:19.518754 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-18 02:36:19.720825 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-18 02:36:19.929045 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-18 02:36:20.123231 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-18 02:36:20.27356 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-18 02:36:20.420576 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-18 02:36:20.658383 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-18 02:36:20.831062 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-18 02:36:21.016144 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-18 02:36:21.201236 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-18 02:36:21.429258 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-18 02:36:21.642892 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-18 02:36:21.849343 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-18 02:36:22.018898 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-18 02:36:22.210518 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-18 02:36:22.347187 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-18 02:36:22.47433 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-18 02:36:22.617099 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-18 02:36:22.775015 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-18 02:36:22.980583 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-18 02:36:23.126135 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-18 02:36:23.337721 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-18 02:36:23.54313 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-18 02:36:23.782383 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-18 02:36:23.996344 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-18 02:36:24.227039 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-18 02:36:24.437242 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-18 02:36:24.593343 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-18 02:36:24.738136 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-18 02:36:24.883743 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-18 02:36:25.077797 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-18 02:36:25.516986 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-18 02:36:25.687961 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-18 02:36:25.86107 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-18 02:36:26.0584 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-18 02:36:26.254238 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-18 02:36:26.459727 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-18 02:36:26.61846 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-18 02:36:26.826047 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-18 02:36:27.033186 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-18 02:36:27.250816 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-18 02:36:27.466009 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-18 02:36:27.662892 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-18 02:36:27.868775 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-18 02:36:28.075823 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-18 02:36:28.282271 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-18 02:36:28.505043 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-18 02:36:28.969522 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-18 02:36:29.17683 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-18 02:36:29.332859 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-18 02:36:29.512143 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-18 02:36:29.725287 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-18 02:36:29.92782 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-18 02:36:30.123877 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-18 02:36:30.346069 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-18 02:36:30.561846 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-18 02:36:30.75227 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-18 02:36:30.962326 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-18 02:36:31.157073 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-18 02:36:31.367744 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-18 02:36:31.550464 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-18 02:36:31.697014 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-18 02:36:31.835887 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-18 02:36:32.042595 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-18 02:36:32.238636 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-18 02:36:32.426626 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-18 02:36:32.558777 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-18 02:36:32.693065 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-18 02:36:32.848251 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-18 02:36:33.058382 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-18 02:36:33.237506 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-18 02:36:33.394141 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-18 02:36:33.563734 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-18 02:36:33.75921 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-18 02:36:33.943536 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-18 02:36:34.153701 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-18 02:36:34.350643 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-18 02:36:34.551178 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-18 02:36:34.748139 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-18 02:36:34.88955 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-18 02:36:35.096032 INFO::Counting total values for each feature
2024-07-18 02:36:35.152407 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-18 02:36:35.555466 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-18 02:36:36.060753 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-18 02:36:36.46162 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-18 02:36:36.52014 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-18 02:36:36.555941 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-18 02:36:36.565353 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-18 02:36:36.591001 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"
2024-07-18 02:36:36.635454 INFO::Writing function arguments to log file
2024-07-18 02:36:36.658835 INFO::Verifying options selected are valid
2024-07-18 02:36:36.660803 INFO::Determining format of input files
2024-07-18 02:36:36.662828 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-18 02:36:36.670919 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-18 02:36:36.673038 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-18 02:36:36.675926 INFO::Filter data based on min abundance and min prevalence
2024-07-18 02:36:36.677822 INFO::Total samples in data: 1595
2024-07-18 02:36:36.679947 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-18 02:36:36.695238 INFO::Total filtered features: 0
2024-07-18 02:36:36.698135 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-18 02:36:36.707011 INFO::Total filtered features with variance filtering: 0
2024-07-18 02:36:36.709462 INFO::Filtered feature names from variance filtering:
2024-07-18 02:36:36.711603 INFO::Running selected normalization method: NONE
2024-07-18 02:36:36.713921 INFO::Bypass z-score application to metadata
2024-07-18 02:36:36.715721 INFO::Running selected transform method: AST
2024-07-18 02:36:36.731829 INFO::Running selected analysis method: LM
2024-07-18 02:36:36.740436 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-18 02:36:36.881685 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-18 02:36:37.101149 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-18 02:36:37.234611 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-18 02:36:37.430598 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-18 02:36:37.651356 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-18 02:36:37.856922 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-18 02:36:38.016963 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-18 02:36:38.187133 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-18 02:36:38.348939 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-18 02:36:38.566506 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-18 02:36:38.777478 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-18 02:36:38.948851 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-18 02:36:39.157515 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-18 02:36:39.365426 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-18 02:36:39.560308 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-18 02:36:39.754638 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-18 02:36:39.916214 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-18 02:36:40.027876 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-18 02:36:40.217 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-18 02:36:40.445215 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-18 02:36:40.650255 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-18 02:36:40.792863 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-18 02:36:40.941425 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-18 02:36:41.1042 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-18 02:36:41.276546 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-18 02:36:41.448144 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-18 02:36:41.576664 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-18 02:36:41.702176 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-18 02:36:41.836365 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-18 02:36:42.036116 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-18 02:36:42.216841 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-18 02:36:42.339191 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-18 02:36:42.4738 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-18 02:36:42.656248 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-18 02:36:42.837558 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-18 02:36:42.965804 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-18 02:36:43.122556 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-18 02:36:43.315609 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-18 02:36:43.524875 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-18 02:36:43.647638 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-18 02:36:43.860097 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-18 02:36:44.00603 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-18 02:36:44.136454 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-18 02:36:44.276679 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-18 02:36:44.460128 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-18 02:36:44.616858 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-18 02:36:44.819827 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-18 02:36:45.014098 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-18 02:36:45.213127 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-18 02:36:45.364265 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-18 02:36:45.490027 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-18 02:36:45.65802 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-18 02:36:45.841657 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-18 02:36:46.031357 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-18 02:36:46.207925 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-18 02:36:46.337168 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-18 02:36:46.521005 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-18 02:36:46.685441 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-18 02:36:46.88519 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-18 02:36:47.022978 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-18 02:36:47.203322 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-18 02:36:47.414892 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-18 02:36:47.573676 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-18 02:36:47.695018 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-18 02:36:47.859365 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-18 02:36:48.041108 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-18 02:36:48.255047 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-18 02:36:48.44781 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-18 02:36:48.642382 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-18 02:36:48.852568 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-18 02:36:49.035357 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-18 02:36:49.248859 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-18 02:36:49.45931 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-18 02:36:49.631489 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-18 02:36:49.690546 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-18 02:36:49.840865 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-18 02:36:49.996506 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-18 02:36:50.148771 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-18 02:36:50.298888 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-18 02:36:50.45591 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-18 02:36:50.604908 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-18 02:36:50.800172 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-18 02:36:51.005607 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-18 02:36:51.155114 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-18 02:36:51.321717 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-18 02:36:51.50183 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-18 02:36:51.64469 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-18 02:36:51.817499 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-18 02:36:51.961663 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-18 02:36:52.141897 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-18 02:36:52.394053 INFO::Counting total values for each feature
2024-07-18 02:36:52.430763 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-18 02:36:52.787325 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-18 02:36:53.218737 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-18 02:36:53.631675 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-18 02:36:53.708038 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-18 02:36:53.78067 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-18 02:36:53.789424 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-18 02:36:53.807641 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  38.59    1.14   39.76

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2110.60 7.10117.89