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CHECK report for Maaslin2 on tokay2

This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Maaslin2 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 968/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.2.0
Lauren McIver
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Maaslin2
Branch: RELEASE_3_11
Last Commit: 9529c31
Last Changed Date: 2020-04-27 15:28:47 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Maaslin2
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Maaslin2_1.2.0.tar.gz
StartedAt: 2020-10-17 05:35:24 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:40:48 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 324.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Maaslin2_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Maaslin2.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.2.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
Maaslin2 88.99   2.26    91.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
Maaslin2 91.73   2.37   94.73
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: OK

Installation output

Maaslin2.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Maaslin2_1.2.0.tar.gz && rm -rf Maaslin2.buildbin-libdir && mkdir Maaslin2.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Maaslin2.buildbin-libdir Maaslin2_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Maaslin2_1.2.0.zip && rm Maaslin2_1.2.0.tar.gz Maaslin2_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  322k  100  322k    0     0  5376k      0 --:--:-- --:--:-- --:--:-- 6086k

install for i386

* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Maaslin2'
    finding HTML links ... done
    Maaslin2                                html  
** 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

install for x64

* installing *source* package 'Maaslin2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Maaslin2' as Maaslin2_1.2.0.zip
* DONE (Maaslin2)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Maaslin2' successfully unpacked and MD5 sums checked

Tests output

Maaslin2.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 figures folder"
2020-10-17 05:39:14 INFO::Writing function arguments to log file
2020-10-17 05:39:14 INFO::Verifying options selected are valid
2020-10-17 05:39:14 INFO::Determining format of input files
2020-10-17 05:39:14 INFO::Input format is data samples as rows and metadata samples as rows
2020-10-17 05:39:14 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-10-17 05:39:14 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2020-10-17 05:39:14 INFO::Running selected normalization method: TSS
2020-10-17 05:39:16 INFO::Filter data based on min abundance and min prevalence
2020-10-17 05:39:16 INFO::Total samples in data: 1595
2020-10-17 05:39:16 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-10-17 05:39:16 INFO::Total filtered features: 0
2020-10-17 05:39:16 INFO::Filtered feature names:
2020-10-17 05:39:16 INFO::Bypass z-score application to metadata
2020-10-17 05:39:16 INFO::Running selected transform method: AST
2020-10-17 05:39:16 INFO::Running selected analysis method: LM
2020-10-17 05:39:16 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-10-17 05:39:18 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-10-17 05:39:18 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-10-17 05:39:18 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-10-17 05:39:18 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-10-17 05:39:19 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-10-17 05:39:19 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-10-17 05:39:19 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-10-17 05:39:19 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-10-17 05:39:19 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-10-17 05:39:19 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-10-17 05:39:20 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-10-17 05:39:20 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-10-17 05:39:20 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-10-17 05:39:20 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-10-17 05:39:20 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-10-17 05:39:21 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-10-17 05:39:21 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-10-17 05:39:21 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-10-17 05:39:21 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-10-17 05:39:21 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-10-17 05:39:22 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-10-17 05:39:22 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-10-17 05:39:22 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-10-17 05:39:22 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-10-17 05:39:23 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-10-17 05:39:23 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-10-17 05:39:23 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-10-17 05:39:23 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-10-17 05:39:23 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-10-17 05:39:24 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-10-17 05:39:24 INFO::Fitting model to feature number 32, Prevotella.copri
2020-10-17 05:39:24 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-10-17 05:39:24 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-10-17 05:39:24 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-10-17 05:39:25 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-10-17 05:39:25 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-10-17 05:39:25 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-10-17 05:39:25 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-10-17 05:39:25 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-10-17 05:39:25 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-10-17 05:39:26 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-10-17 05:39:26 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-10-17 05:39:26 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-10-17 05:39:26 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-10-17 05:39:26 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-10-17 05:39:26 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-10-17 05:39:27 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-10-17 05:39:27 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-10-17 05:39:27 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-10-17 05:39:27 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-10-17 05:39:27 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-10-17 05:39:27 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-10-17 05:39:28 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-10-17 05:39:28 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-10-17 05:39:28 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-10-17 05:39:28 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-10-17 05:39:28 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-10-17 05:39:29 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-10-17 05:39:29 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-10-17 05:39:29 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-10-17 05:39:29 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-10-17 05:39:29 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-10-17 05:39:29 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-10-17 05:39:30 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-10-17 05:39:30 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-10-17 05:39:30 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-10-17 05:39:30 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-10-17 05:39:30 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-10-17 05:39:30 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-10-17 05:39:31 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-10-17 05:39:31 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-10-17 05:39:31 INFO::Fitting model to feature number 73, Dialister.invisus
2020-10-17 05:39:31 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-10-17 05:39:31 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-10-17 05:39:31 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-10-17 05:39:32 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-10-17 05:39:32 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-10-17 05:39:32 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-10-17 05:39:32 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-10-17 05:39:33 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-10-17 05:39:33 INFO::Fitting model to feature number 82, Escherichia.coli
2020-10-17 05:39:33 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-10-17 05:39:33 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-10-17 05:39:33 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-10-17 05:39:33 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-10-17 05:39:34 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-10-17 05:39:34 INFO::Counting total values for each feature
2020-10-17 05:39:34 INFO::Writing residuals to file output/residuals.rds
2020-10-17 05:39:34 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2020-10-17 05:39:34 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 figures folder"
2020-10-17 05:39:34 INFO::Writing function arguments to log file
2020-10-17 05:39:34 INFO::Verifying options selected are valid
2020-10-17 05:39:34 INFO::Determining format of input files
2020-10-17 05:39:34 INFO::Input format is data samples as rows and metadata samples as rows
2020-10-17 05:39:34 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-10-17 05:39:34 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2020-10-17 05:39:34 INFO::Running selected normalization method: NONE
2020-10-17 05:39:34 INFO::Filter data based on min abundance and min prevalence
2020-10-17 05:39:34 INFO::Total samples in data: 1595
2020-10-17 05:39:34 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-10-17 05:39:34 INFO::Total filtered features: 0
2020-10-17 05:39:34 INFO::Filtered feature names:
2020-10-17 05:39:34 INFO::Bypass z-score application to metadata
2020-10-17 05:39:34 INFO::Running selected transform method: AST
2020-10-17 05:39:34 INFO::Running selected analysis method: LM
2020-10-17 05:39:34 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-10-17 05:39:34 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-10-17 05:39:35 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-10-17 05:39:35 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-10-17 05:39:35 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-10-17 05:39:35 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-10-17 05:39:35 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-10-17 05:39:36 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-10-17 05:39:36 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-10-17 05:39:36 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-10-17 05:39:36 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-10-17 05:39:36 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-10-17 05:39:36 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-10-17 05:39:37 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-10-17 05:39:37 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-10-17 05:39:37 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-10-17 05:39:37 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-10-17 05:39:37 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-10-17 05:39:37 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-10-17 05:39:38 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-10-17 05:39:38 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-10-17 05:39:38 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-10-17 05:39:38 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-10-17 05:39:38 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-10-17 05:39:38 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-10-17 05:39:39 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-10-17 05:39:39 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-10-17 05:39:39 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-10-17 05:39:39 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-10-17 05:39:39 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-10-17 05:39:40 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-10-17 05:39:40 INFO::Fitting model to feature number 32, Prevotella.copri
2020-10-17 05:39:40 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-10-17 05:39:40 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-10-17 05:39:40 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-10-17 05:39:41 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-10-17 05:39:41 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-10-17 05:39:41 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-10-17 05:39:41 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-10-17 05:39:41 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-10-17 05:39:42 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-10-17 05:39:42 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-10-17 05:39:42 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-10-17 05:39:42 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-10-17 05:39:42 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-10-17 05:39:42 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-10-17 05:39:43 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-10-17 05:39:43 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-10-17 05:39:43 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-10-17 05:39:43 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-10-17 05:39:43 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-10-17 05:39:44 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-10-17 05:39:44 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-10-17 05:39:44 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-10-17 05:39:44 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-10-17 05:39:44 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-10-17 05:39:44 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-10-17 05:39:45 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-10-17 05:39:45 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-10-17 05:39:45 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-10-17 05:39:45 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-10-17 05:39:45 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-10-17 05:39:45 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-10-17 05:39:46 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-10-17 05:39:46 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-10-17 05:39:46 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-10-17 05:39:46 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-10-17 05:39:46 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-10-17 05:39:46 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-10-17 05:39:47 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-10-17 05:39:47 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-10-17 05:39:47 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-10-17 05:39:47 INFO::Fitting model to feature number 73, Dialister.invisus
2020-10-17 05:39:47 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-10-17 05:39:48 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-10-17 05:39:48 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-10-17 05:39:48 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-10-17 05:39:48 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-10-17 05:39:48 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-10-17 05:39:48 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-10-17 05:39:49 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-10-17 05:39:49 INFO::Fitting model to feature number 82, Escherichia.coli
2020-10-17 05:39:49 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-10-17 05:39:49 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-10-17 05:39:49 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-10-17 05:39:49 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-10-17 05:39:50 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-10-17 05:39:50 INFO::Counting total values for each feature
2020-10-17 05:39:50 INFO::Writing residuals to file output2/residuals.rds
2020-10-17 05:39:50 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2020-10-17 05:39:50 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
== testthat results  ===========================================================
[ OK: 12 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  37.57    0.53   38.15

Maaslin2.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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"
[1] "Creating output figures folder"
2020-10-17 05:39:53 INFO::Writing function arguments to log file
2020-10-17 05:39:53 INFO::Verifying options selected are valid
2020-10-17 05:39:53 INFO::Determining format of input files
2020-10-17 05:39:53 INFO::Input format is data samples as rows and metadata samples as rows
2020-10-17 05:39:53 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-10-17 05:39:53 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2020-10-17 05:39:53 INFO::Running selected normalization method: TSS
2020-10-17 05:39:54 INFO::Filter data based on min abundance and min prevalence
2020-10-17 05:39:54 INFO::Total samples in data: 1595
2020-10-17 05:39:54 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-10-17 05:39:54 INFO::Total filtered features: 0
2020-10-17 05:39:54 INFO::Filtered feature names:
2020-10-17 05:39:54 INFO::Bypass z-score application to metadata
2020-10-17 05:39:54 INFO::Running selected transform method: AST
2020-10-17 05:39:54 INFO::Running selected analysis method: LM
2020-10-17 05:39:54 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-10-17 05:39:56 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-10-17 05:39:56 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-10-17 05:39:56 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-10-17 05:39:57 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-10-17 05:39:57 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-10-17 05:39:57 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-10-17 05:39:57 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-10-17 05:39:57 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-10-17 05:39:58 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-10-17 05:39:58 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-10-17 05:39:58 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-10-17 05:39:58 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-10-17 05:39:59 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-10-17 05:39:59 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-10-17 05:39:59 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-10-17 05:40:00 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-10-17 05:40:00 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-10-17 05:40:00 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-10-17 05:40:00 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-10-17 05:40:01 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-10-17 05:40:01 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-10-17 05:40:01 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-10-17 05:40:01 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-10-17 05:40:02 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-10-17 05:40:02 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-10-17 05:40:02 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-10-17 05:40:02 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-10-17 05:40:02 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-10-17 05:40:03 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-10-17 05:40:03 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-10-17 05:40:03 INFO::Fitting model to feature number 32, Prevotella.copri
2020-10-17 05:40:03 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-10-17 05:40:04 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-10-17 05:40:04 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-10-17 05:40:04 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-10-17 05:40:04 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-10-17 05:40:04 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-10-17 05:40:05 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-10-17 05:40:05 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-10-17 05:40:05 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-10-17 05:40:05 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-10-17 05:40:06 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-10-17 05:40:06 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-10-17 05:40:06 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-10-17 05:40:06 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-10-17 05:40:07 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-10-17 05:40:07 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-10-17 05:40:07 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-10-17 05:40:07 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-10-17 05:40:08 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-10-17 05:40:08 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-10-17 05:40:08 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-10-17 05:40:09 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-10-17 05:40:09 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-10-17 05:40:09 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-10-17 05:40:09 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-10-17 05:40:10 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-10-17 05:40:10 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-10-17 05:40:10 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-10-17 05:40:10 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-10-17 05:40:11 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-10-17 05:40:11 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-10-17 05:40:11 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-10-17 05:40:11 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-10-17 05:40:12 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-10-17 05:40:12 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-10-17 05:40:12 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-10-17 05:40:12 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-10-17 05:40:12 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-10-17 05:40:13 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-10-17 05:40:13 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-10-17 05:40:13 INFO::Fitting model to feature number 73, Dialister.invisus
2020-10-17 05:40:13 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-10-17 05:40:13 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-10-17 05:40:14 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-10-17 05:40:14 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-10-17 05:40:14 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-10-17 05:40:14 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-10-17 05:40:14 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-10-17 05:40:15 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-10-17 05:40:15 INFO::Fitting model to feature number 82, Escherichia.coli
2020-10-17 05:40:15 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-10-17 05:40:15 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-10-17 05:40:15 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-10-17 05:40:16 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-10-17 05:40:16 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-10-17 05:40:16 INFO::Counting total values for each feature
2020-10-17 05:40:16 INFO::Writing residuals to file output/residuals.rds
2020-10-17 05:40:16 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2020-10-17 05:40:16 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 figures folder"
2020-10-17 05:40:16 INFO::Writing function arguments to log file
2020-10-17 05:40:16 INFO::Verifying options selected are valid
2020-10-17 05:40:16 INFO::Determining format of input files
2020-10-17 05:40:16 INFO::Input format is data samples as rows and metadata samples as rows
2020-10-17 05:40:16 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-10-17 05:40:16 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2020-10-17 05:40:16 INFO::Running selected normalization method: NONE
2020-10-17 05:40:16 INFO::Filter data based on min abundance and min prevalence
2020-10-17 05:40:16 INFO::Total samples in data: 1595
2020-10-17 05:40:16 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-10-17 05:40:16 INFO::Total filtered features: 0
2020-10-17 05:40:16 INFO::Filtered feature names:
2020-10-17 05:40:16 INFO::Bypass z-score application to metadata
2020-10-17 05:40:16 INFO::Running selected transform method: AST
2020-10-17 05:40:16 INFO::Running selected analysis method: LM
2020-10-17 05:40:16 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-10-17 05:40:17 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-10-17 05:40:17 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-10-17 05:40:17 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-10-17 05:40:17 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-10-17 05:40:18 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-10-17 05:40:18 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-10-17 05:40:18 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-10-17 05:40:18 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-10-17 05:40:19 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-10-17 05:40:19 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-10-17 05:40:20 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-10-17 05:40:20 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-10-17 05:40:21 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-10-17 05:40:21 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-10-17 05:40:22 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-10-17 05:40:22 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-10-17 05:40:22 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-10-17 05:40:23 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-10-17 05:40:23 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-10-17 05:40:23 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-10-17 05:40:24 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-10-17 05:40:24 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-10-17 05:40:24 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-10-17 05:40:25 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-10-17 05:40:25 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-10-17 05:40:25 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-10-17 05:40:26 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-10-17 05:40:26 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-10-17 05:40:26 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-10-17 05:40:26 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-10-17 05:40:27 INFO::Fitting model to feature number 32, Prevotella.copri
2020-10-17 05:40:27 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-10-17 05:40:27 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-10-17 05:40:27 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-10-17 05:40:28 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-10-17 05:40:28 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-10-17 05:40:28 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-10-17 05:40:29 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-10-17 05:40:29 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-10-17 05:40:29 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-10-17 05:40:29 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-10-17 05:40:29 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-10-17 05:40:29 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-10-17 05:40:30 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-10-17 05:40:30 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-10-17 05:40:30 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-10-17 05:40:30 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-10-17 05:40:30 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-10-17 05:40:30 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-10-17 05:40:31 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-10-17 05:40:31 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-10-17 05:40:31 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-10-17 05:40:31 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-10-17 05:40:32 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-10-17 05:40:32 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-10-17 05:40:32 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-10-17 05:40:32 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-10-17 05:40:32 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-10-17 05:40:33 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-10-17 05:40:33 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-10-17 05:40:33 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-10-17 05:40:34 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-10-17 05:40:34 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-10-17 05:40:34 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-10-17 05:40:34 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-10-17 05:40:34 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-10-17 05:40:35 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-10-17 05:40:35 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-10-17 05:40:35 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-10-17 05:40:35 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-10-17 05:40:36 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-10-17 05:40:36 INFO::Fitting model to feature number 73, Dialister.invisus
2020-10-17 05:40:36 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-10-17 05:40:37 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-10-17 05:40:37 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-10-17 05:40:37 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-10-17 05:40:37 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-10-17 05:40:37 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-10-17 05:40:37 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-10-17 05:40:38 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-10-17 05:40:38 INFO::Fitting model to feature number 82, Escherichia.coli
2020-10-17 05:40:38 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-10-17 05:40:38 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-10-17 05:40:39 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-10-17 05:40:39 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-10-17 05:40:39 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-10-17 05:40:39 INFO::Counting total values for each feature
2020-10-17 05:40:39 INFO::Writing residuals to file output2/residuals.rds
2020-10-17 05:40:39 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2020-10-17 05:40:39 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
== testthat results  ===========================================================
[ OK: 12 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  48.10    0.50   49.09

Example timings

Maaslin2.Rcheck/examples_i386/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin288.99 2.2691.70

Maaslin2.Rcheck/examples_x64/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin291.73 2.3794.73