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This page was generated on 2023-01-02 09:00:36 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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

CHECK results for Maaslin2 on palomino5


To the developers/maintainers of the Maaslin2 package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1055/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.13.0  (landing page)
Lauren McIver
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: master
git_last_commit: 56c7729
git_last_commit_date: 2022-11-01 11:20:14 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: Maaslin2
Version: 1.13.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Maaslin2_1.13.0.tar.gz
StartedAt: 2022-12-29 00:59:18 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:01:44 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 145.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Maaslin2_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.13.0'
* 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 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 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: no visible global function definition for 'type.convert'
maaslin2_association_plots: no visible binding for global variable
  'xnames'
Undefined global functions or variables:
  type.convert xnames
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
* 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 75.19   6.29   81.77
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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"
2022-12-29 01:01:11.157815 INFO::Writing function arguments to log file
2022-12-29 01:01:11.187442 INFO::Verifying options selected are valid
2022-12-29 01:01:11.217433 INFO::Determining format of input files
2022-12-29 01:01:11.21944 INFO::Input format is data samples as rows and metadata samples as rows
2022-12-29 01:01:11.226062 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2022-12-29 01:01:11.233796 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2022-12-29 01:01:11.236522 INFO::Filter data based on min abundance and min prevalence
2022-12-29 01:01:11.238135 INFO::Total samples in data: 1595
2022-12-29 01:01:11.239724 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2022-12-29 01:01:11.244663 INFO::Total filtered features: 0
2022-12-29 01:01:11.24645 INFO::Filtered feature names from abundance and prevalence filtering:
2022-12-29 01:01:11.254135 INFO::Total filtered features with variance filtering: 0
2022-12-29 01:01:11.255887 INFO::Filtered feature names from variance filtering:
2022-12-29 01:01:11.257525 INFO::Running selected normalization method: TSS
2022-12-29 01:01:12.335086 INFO::Bypass z-score application to metadata
2022-12-29 01:01:12.337051 INFO::Running selected transform method: AST
2022-12-29 01:01:12.352367 INFO::Running selected analysis method: LM
2022-12-29 01:01:12.811733 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2022-12-29 01:01:13.167552 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2022-12-29 01:01:13.300453 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2022-12-29 01:01:13.422746 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2022-12-29 01:01:13.553557 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2022-12-29 01:01:13.687534 INFO::Fitting model to feature number 6, Bacteroides.caccae
2022-12-29 01:01:13.819697 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2022-12-29 01:01:13.970151 INFO::Fitting model to feature number 8, Bacteroides.dorei
2022-12-29 01:01:14.112989 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2022-12-29 01:01:14.244642 INFO::Fitting model to feature number 10, Bacteroides.faecis
2022-12-29 01:01:14.367285 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2022-12-29 01:01:14.490347 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2022-12-29 01:01:14.61588 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2022-12-29 01:01:14.748607 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2022-12-29 01:01:14.87916 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2022-12-29 01:01:15.006136 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2022-12-29 01:01:15.1272 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2022-12-29 01:01:15.252135 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2022-12-29 01:01:15.382368 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2022-12-29 01:01:15.495706 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2022-12-29 01:01:15.612403 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2022-12-29 01:01:15.744138 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2022-12-29 01:01:15.862139 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2022-12-29 01:01:15.977069 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2022-12-29 01:01:16.098844 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2022-12-29 01:01:16.220662 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2022-12-29 01:01:16.332355 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2022-12-29 01:01:16.457134 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2022-12-29 01:01:16.579259 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2022-12-29 01:01:16.699208 INFO::Fitting model to feature number 30, Paraprevotella.clara
2022-12-29 01:01:16.82375 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2022-12-29 01:01:16.982724 INFO::Fitting model to feature number 32, Prevotella.copri
2022-12-29 01:01:17.11923 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2022-12-29 01:01:17.249614 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2022-12-29 01:01:17.377233 INFO::Fitting model to feature number 35, Alistipes.putredinis
2022-12-29 01:01:17.525426 INFO::Fitting model to feature number 36, Alistipes.shahii
2022-12-29 01:01:17.650352 INFO::Fitting model to feature number 37, Alistipes.unclassified
2022-12-29 01:01:17.778348 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2022-12-29 01:01:17.918371 INFO::Fitting model to feature number 39, Clostridium.bolteae
2022-12-29 01:01:18.058666 INFO::Fitting model to feature number 40, Clostridium.citroniae
2022-12-29 01:01:18.265514 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2022-12-29 01:01:18.438133 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2022-12-29 01:01:18.565307 INFO::Fitting model to feature number 43, Clostridium.leptum
2022-12-29 01:01:18.680008 INFO::Fitting model to feature number 44, Clostridium.nexile
2022-12-29 01:01:18.799779 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2022-12-29 01:01:18.928013 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2022-12-29 01:01:19.056985 INFO::Fitting model to feature number 47, Eubacterium.eligens
2022-12-29 01:01:19.186015 INFO::Fitting model to feature number 48, Eubacterium.hallii
2022-12-29 01:01:19.31017 INFO::Fitting model to feature number 49, Eubacterium.rectale
2022-12-29 01:01:19.452626 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2022-12-29 01:01:19.61721 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2022-12-29 01:01:19.817062 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2022-12-29 01:01:19.944359 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2022-12-29 01:01:20.073436 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2022-12-29 01:01:20.19247 INFO::Fitting model to feature number 55, Ruminococcus.torques
2022-12-29 01:01:20.337353 INFO::Fitting model to feature number 56, Coprococcus.comes
2022-12-29 01:01:20.461138 INFO::Fitting model to feature number 57, Dorea.longicatena
2022-12-29 01:01:20.578807 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2022-12-29 01:01:20.701455 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2022-12-29 01:01:20.82657 INFO::Fitting model to feature number 60, Roseburia.hominis
2022-12-29 01:01:20.941518 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2022-12-29 01:01:21.060458 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2022-12-29 01:01:21.353261 INFO::Fitting model to feature number 63, Roseburia.unclassified
2022-12-29 01:01:21.47223 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2022-12-29 01:01:21.589387 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2022-12-29 01:01:21.708625 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2022-12-29 01:01:21.824597 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2022-12-29 01:01:21.936281 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2022-12-29 01:01:22.057698 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2022-12-29 01:01:22.177725 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2022-12-29 01:01:22.297259 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2022-12-29 01:01:22.416225 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2022-12-29 01:01:22.530638 INFO::Fitting model to feature number 73, Dialister.invisus
2022-12-29 01:01:22.644784 INFO::Fitting model to feature number 74, Veillonella.atypica
2022-12-29 01:01:22.766021 INFO::Fitting model to feature number 75, Veillonella.dispar
2022-12-29 01:01:22.885313 INFO::Fitting model to feature number 76, Veillonella.parvula
2022-12-29 01:01:23.001853 INFO::Fitting model to feature number 77, Veillonella.unclassified
2022-12-29 01:01:23.12345 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2022-12-29 01:01:23.245703 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2022-12-29 01:01:23.370548 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2022-12-29 01:01:23.487107 INFO::Fitting model to feature number 81, Bilophila.unclassified
2022-12-29 01:01:23.608963 INFO::Fitting model to feature number 82, Escherichia.coli
2022-12-29 01:01:23.733014 INFO::Fitting model to feature number 83, Escherichia.unclassified
2022-12-29 01:01:23.872934 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2022-12-29 01:01:24.028672 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2022-12-29 01:01:24.142807 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2022-12-29 01:01:24.256356 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2022-12-29 01:01:24.427275 INFO::Counting total values for each feature
2022-12-29 01:01:24.465241 INFO::Writing residuals to file output/residuals.rds
2022-12-29 01:01:24.515198 INFO::Writing fitted values to file output/fitted.rds
2022-12-29 01:01:24.54257 INFO::Writing extracted random effects to file output/ranef.rds
2022-12-29 01:01:24.549231 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2022-12-29 01:01:24.563595 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"
2022-12-29 01:01:24.583664 INFO::Writing function arguments to log file
2022-12-29 01:01:24.598356 INFO::Verifying options selected are valid
2022-12-29 01:01:24.60005 INFO::Determining format of input files
2022-12-29 01:01:24.601937 INFO::Input format is data samples as rows and metadata samples as rows
2022-12-29 01:01:24.608116 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2022-12-29 01:01:24.60984 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2022-12-29 01:01:24.617351 INFO::Filter data based on min abundance and min prevalence
2022-12-29 01:01:24.61898 INFO::Total samples in data: 1595
2022-12-29 01:01:24.62052 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2022-12-29 01:01:24.62438 INFO::Total filtered features: 0
2022-12-29 01:01:24.625971 INFO::Filtered feature names from abundance and prevalence filtering:
2022-12-29 01:01:24.632771 INFO::Total filtered features with variance filtering: 0
2022-12-29 01:01:24.6345 INFO::Filtered feature names from variance filtering:
2022-12-29 01:01:24.636032 INFO::Running selected normalization method: NONE
2022-12-29 01:01:24.637505 INFO::Bypass z-score application to metadata
2022-12-29 01:01:24.638969 INFO::Running selected transform method: AST
2022-12-29 01:01:24.654855 INFO::Running selected analysis method: LM
2022-12-29 01:01:24.657291 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2022-12-29 01:01:24.770644 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2022-12-29 01:01:25.069096 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2022-12-29 01:01:25.177819 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2022-12-29 01:01:25.295976 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2022-12-29 01:01:25.416893 INFO::Fitting model to feature number 6, Bacteroides.caccae
2022-12-29 01:01:25.542362 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2022-12-29 01:01:25.655761 INFO::Fitting model to feature number 8, Bacteroides.dorei
2022-12-29 01:01:25.767667 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2022-12-29 01:01:25.89088 INFO::Fitting model to feature number 10, Bacteroides.faecis
2022-12-29 01:01:26.004923 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2022-12-29 01:01:26.162071 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2022-12-29 01:01:26.311974 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2022-12-29 01:01:26.440926 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2022-12-29 01:01:26.555283 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2022-12-29 01:01:26.671038 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2022-12-29 01:01:26.784196 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2022-12-29 01:01:26.92899 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2022-12-29 01:01:27.041582 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2022-12-29 01:01:27.152366 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2022-12-29 01:01:27.285602 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2022-12-29 01:01:27.403943 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2022-12-29 01:01:27.546031 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2022-12-29 01:01:27.700849 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2022-12-29 01:01:27.898264 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2022-12-29 01:01:28.029745 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2022-12-29 01:01:28.146446 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2022-12-29 01:01:28.259597 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2022-12-29 01:01:28.367752 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2022-12-29 01:01:28.480285 INFO::Fitting model to feature number 30, Paraprevotella.clara
2022-12-29 01:01:28.592213 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2022-12-29 01:01:28.70411 INFO::Fitting model to feature number 32, Prevotella.copri
2022-12-29 01:01:28.826034 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2022-12-29 01:01:28.936895 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2022-12-29 01:01:29.050368 INFO::Fitting model to feature number 35, Alistipes.putredinis
2022-12-29 01:01:29.171982 INFO::Fitting model to feature number 36, Alistipes.shahii
2022-12-29 01:01:29.285728 INFO::Fitting model to feature number 37, Alistipes.unclassified
2022-12-29 01:01:29.398729 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2022-12-29 01:01:29.513839 INFO::Fitting model to feature number 39, Clostridium.bolteae
2022-12-29 01:01:29.628409 INFO::Fitting model to feature number 40, Clostridium.citroniae
2022-12-29 01:01:29.739517 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2022-12-29 01:01:29.854267 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2022-12-29 01:01:29.971976 INFO::Fitting model to feature number 43, Clostridium.leptum
2022-12-29 01:01:30.090252 INFO::Fitting model to feature number 44, Clostridium.nexile
2022-12-29 01:01:30.204788 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2022-12-29 01:01:30.317822 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2022-12-29 01:01:30.44009 INFO::Fitting model to feature number 47, Eubacterium.eligens
2022-12-29 01:01:30.549223 INFO::Fitting model to feature number 48, Eubacterium.hallii
2022-12-29 01:01:30.662489 INFO::Fitting model to feature number 49, Eubacterium.rectale
2022-12-29 01:01:30.780763 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2022-12-29 01:01:30.887329 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2022-12-29 01:01:31.004826 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2022-12-29 01:01:31.129694 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2022-12-29 01:01:31.267462 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2022-12-29 01:01:31.376178 INFO::Fitting model to feature number 55, Ruminococcus.torques
2022-12-29 01:01:31.494886 INFO::Fitting model to feature number 56, Coprococcus.comes
2022-12-29 01:01:31.606642 INFO::Fitting model to feature number 57, Dorea.longicatena
2022-12-29 01:01:31.717585 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2022-12-29 01:01:31.835017 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2022-12-29 01:01:31.951333 INFO::Fitting model to feature number 60, Roseburia.hominis
2022-12-29 01:01:32.062468 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2022-12-29 01:01:32.190053 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2022-12-29 01:01:32.299094 INFO::Fitting model to feature number 63, Roseburia.unclassified
2022-12-29 01:01:32.413409 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2022-12-29 01:01:32.533405 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2022-12-29 01:01:32.646265 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2022-12-29 01:01:32.757707 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2022-12-29 01:01:32.873474 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2022-12-29 01:01:32.988592 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2022-12-29 01:01:33.103866 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2022-12-29 01:01:33.277034 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2022-12-29 01:01:33.465619 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2022-12-29 01:01:33.621434 INFO::Fitting model to feature number 73, Dialister.invisus
2022-12-29 01:01:33.735166 INFO::Fitting model to feature number 74, Veillonella.atypica
2022-12-29 01:01:33.866135 INFO::Fitting model to feature number 75, Veillonella.dispar
2022-12-29 01:01:33.982862 INFO::Fitting model to feature number 76, Veillonella.parvula
2022-12-29 01:01:34.10208 INFO::Fitting model to feature number 77, Veillonella.unclassified
2022-12-29 01:01:34.386055 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2022-12-29 01:01:34.499585 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2022-12-29 01:01:34.61906 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2022-12-29 01:01:34.73527 INFO::Fitting model to feature number 81, Bilophila.unclassified
2022-12-29 01:01:34.856402 INFO::Fitting model to feature number 82, Escherichia.coli
2022-12-29 01:01:34.976367 INFO::Fitting model to feature number 83, Escherichia.unclassified
2022-12-29 01:01:35.083971 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2022-12-29 01:01:35.195115 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2022-12-29 01:01:35.306816 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2022-12-29 01:01:35.425506 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2022-12-29 01:01:35.566003 INFO::Counting total values for each feature
2022-12-29 01:01:35.587866 INFO::Writing residuals to file output2/residuals.rds
2022-12-29 01:01:35.655077 INFO::Writing fitted values to file output2/fitted.rds
2022-12-29 01:01:35.719252 INFO::Writing extracted random effects to file output2/ranef.rds
2022-12-29 01:01:35.725948 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2022-12-29 01:01:35.73685 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 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  25.03    0.70   25.68

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin275.19 6.2981.77