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CHECK report for Maaslin2 on tokay1

This page was generated on 2021-05-06 12:32:05 -0400 (Thu, 06 May 2021).

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 983/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.4.0  (landing page)
Lauren McIver
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Maaslin2
Branch: RELEASE_3_12
Last Commit: a352d2d
Last Changed Date: 2020-10-27 11:47:47 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Maaslin2
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Maaslin2_1.4.0.tar.gz
StartedAt: 2021-05-06 04:11:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:17:11 -0400 (Thu, 06 May 2021)
EllapsedTime: 348.3 seconds
RetCode: 0
Status:   OK   
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Maaslin2_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Maaslin2.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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 ... NOTE
Missing or unexported object: 'cplm::zcpglm'
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 100.05   5.13   105.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
Maaslin2 105.2   4.71  110.06
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Maaslin2_1.4.0.tar.gz && rm -rf Maaslin2.buildbin-libdir && mkdir Maaslin2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Maaslin2.buildbin-libdir Maaslin2_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Maaslin2_1.4.0.zip && rm Maaslin2_1.4.0.tar.gz Maaslin2_1.4.0.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  320k  100  320k    0     0  11.6M      0 --:--:-- --:--:-- --:--:-- 12.0M

install for i386

* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.2
Current Matrix version is 1.3.3
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** 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_1.4.0.zip
* DONE (Maaslin2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Maaslin2' successfully unpacked and MD5 sums checked

Tests output

Maaslin2.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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"
2021-05-06 04:15:46 INFO::Writing function arguments to log file
2021-05-06 04:15:46 INFO::Verifying options selected are valid
2021-05-06 04:15:46 INFO::Determining format of input files
2021-05-06 04:15:46 INFO::Input format is data samples as rows and metadata samples as rows
2021-05-06 04:15:46 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-05-06 04:15:46 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2021-05-06 04:15:46 INFO::Filter data based on min abundance and min prevalence
2021-05-06 04:15:46 INFO::Total samples in data: 1595
2021-05-06 04:15:46 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-05-06 04:15:46 INFO::Total filtered features: 0
2021-05-06 04:15:46 INFO::Filtered feature names from abundance and prevalence filtering:
2021-05-06 04:15:46 INFO::Running selected normalization method: TSS
2021-05-06 04:15:47 INFO::Total filtered features with variance filtering: 0
2021-05-06 04:15:47 INFO::Filtered feature names from variance filtering:
2021-05-06 04:15:47 INFO::Bypass z-score application to metadata
2021-05-06 04:15:47 INFO::Running selected transform method: AST
2021-05-06 04:15:47 INFO::Running selected analysis method: LM
2021-05-06 04:15:47 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-05-06 04:15:49 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-05-06 04:15:49 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-05-06 04:15:49 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-05-06 04:15:49 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-05-06 04:15:50 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-05-06 04:15:50 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-05-06 04:15:50 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-05-06 04:15:50 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-05-06 04:15:50 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-05-06 04:15:50 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-05-06 04:15:51 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-05-06 04:15:51 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-05-06 04:15:51 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-05-06 04:15:51 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-05-06 04:15:51 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-05-06 04:15:52 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-05-06 04:15:52 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-05-06 04:15:52 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-05-06 04:15:52 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-05-06 04:15:52 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-05-06 04:15:53 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-05-06 04:15:53 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-05-06 04:15:53 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-05-06 04:15:53 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-05-06 04:15:53 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-05-06 04:15:53 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-05-06 04:15:54 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-05-06 04:15:54 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-05-06 04:15:54 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-05-06 04:15:54 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-05-06 04:15:54 INFO::Fitting model to feature number 32, Prevotella.copri
2021-05-06 04:15:54 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-05-06 04:15:55 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-05-06 04:15:55 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-05-06 04:15:55 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-05-06 04:15:55 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-05-06 04:15:55 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-05-06 04:15:55 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-05-06 04:15:56 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-05-06 04:15:56 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-05-06 04:15:56 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-05-06 04:15:56 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-05-06 04:15:56 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-05-06 04:15:56 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-05-06 04:15:57 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-05-06 04:15:57 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-05-06 04:15:57 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-05-06 04:15:57 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-05-06 04:15:58 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-05-06 04:15:58 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-05-06 04:15:58 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-05-06 04:15:58 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-05-06 04:15:59 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-05-06 04:15:59 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-05-06 04:15:59 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-05-06 04:16:00 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-05-06 04:16:00 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-05-06 04:16:00 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-05-06 04:16:00 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-05-06 04:16:01 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-05-06 04:16:01 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-05-06 04:16:01 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-05-06 04:16:02 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-05-06 04:16:02 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-05-06 04:16:02 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-05-06 04:16:02 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-05-06 04:16:03 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-05-06 04:16:03 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-05-06 04:16:03 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-05-06 04:16:04 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-05-06 04:16:04 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-05-06 04:16:04 INFO::Fitting model to feature number 73, Dialister.invisus
2021-05-06 04:16:04 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-05-06 04:16:05 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-05-06 04:16:05 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-05-06 04:16:05 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-05-06 04:16:05 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-05-06 04:16:06 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-05-06 04:16:06 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-05-06 04:16:06 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-05-06 04:16:06 INFO::Fitting model to feature number 82, Escherichia.coli
2021-05-06 04:16:06 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-05-06 04:16:07 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-05-06 04:16:07 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-05-06 04:16:07 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-05-06 04:16:07 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-05-06 04:16:08 INFO::Counting total values for each feature
2021-05-06 04:16:08 INFO::Writing residuals to file output/residuals.rds
2021-05-06 04:16:08 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2021-05-06 04:16:08 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"
2021-05-06 04:16:08 INFO::Writing function arguments to log file
2021-05-06 04:16:08 INFO::Verifying options selected are valid
2021-05-06 04:16:08 INFO::Determining format of input files
2021-05-06 04:16:08 INFO::Input format is data samples as rows and metadata samples as rows
2021-05-06 04:16:08 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-05-06 04:16:08 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2021-05-06 04:16:08 INFO::Filter data based on min abundance and min prevalence
2021-05-06 04:16:08 INFO::Total samples in data: 1595
2021-05-06 04:16:08 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-05-06 04:16:08 INFO::Total filtered features: 0
2021-05-06 04:16:08 INFO::Filtered feature names from abundance and prevalence filtering:
2021-05-06 04:16:08 INFO::Running selected normalization method: NONE
2021-05-06 04:16:08 INFO::Total filtered features with variance filtering: 0
2021-05-06 04:16:08 INFO::Filtered feature names from variance filtering:
2021-05-06 04:16:08 INFO::Bypass z-score application to metadata
2021-05-06 04:16:08 INFO::Running selected transform method: AST
2021-05-06 04:16:08 INFO::Running selected analysis method: LM
2021-05-06 04:16:08 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-05-06 04:16:08 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-05-06 04:16:08 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-05-06 04:16:08 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-05-06 04:16:09 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-05-06 04:16:09 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-05-06 04:16:09 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-05-06 04:16:09 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-05-06 04:16:09 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-05-06 04:16:09 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-05-06 04:16:10 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-05-06 04:16:10 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-05-06 04:16:10 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-05-06 04:16:10 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-05-06 04:16:10 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-05-06 04:16:11 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-05-06 04:16:11 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-05-06 04:16:11 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-05-06 04:16:11 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-05-06 04:16:12 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-05-06 04:16:12 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-05-06 04:16:12 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-05-06 04:16:12 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-05-06 04:16:13 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-05-06 04:16:13 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-05-06 04:16:13 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-05-06 04:16:13 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-05-06 04:16:13 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-05-06 04:16:14 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-05-06 04:16:14 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-05-06 04:16:14 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-05-06 04:16:14 INFO::Fitting model to feature number 32, Prevotella.copri
2021-05-06 04:16:15 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-05-06 04:16:15 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-05-06 04:16:15 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-05-06 04:16:15 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-05-06 04:16:16 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-05-06 04:16:16 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-05-06 04:16:16 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-05-06 04:16:16 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-05-06 04:16:17 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-05-06 04:16:17 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-05-06 04:16:17 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-05-06 04:16:17 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-05-06 04:16:18 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-05-06 04:16:18 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-05-06 04:16:18 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-05-06 04:16:18 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-05-06 04:16:18 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-05-06 04:16:18 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-05-06 04:16:19 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-05-06 04:16:19 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-05-06 04:16:19 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-05-06 04:16:19 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-05-06 04:16:19 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-05-06 04:16:20 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-05-06 04:16:20 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-05-06 04:16:20 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-05-06 04:16:20 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-05-06 04:16:20 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-05-06 04:16:20 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-05-06 04:16:21 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-05-06 04:16:21 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-05-06 04:16:21 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-05-06 04:16:21 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-05-06 04:16:21 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-05-06 04:16:21 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-05-06 04:16:22 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-05-06 04:16:22 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-05-06 04:16:22 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-05-06 04:16:22 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-05-06 04:16:23 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-05-06 04:16:23 INFO::Fitting model to feature number 73, Dialister.invisus
2021-05-06 04:16:23 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-05-06 04:16:24 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-05-06 04:16:24 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-05-06 04:16:24 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-05-06 04:16:24 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-05-06 04:16:24 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-05-06 04:16:25 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-05-06 04:16:25 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-05-06 04:16:25 INFO::Fitting model to feature number 82, Escherichia.coli
2021-05-06 04:16:25 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-05-06 04:16:26 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-05-06 04:16:26 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-05-06 04:16:26 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-05-06 04:16:26 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-05-06 04:16:26 INFO::Counting total values for each feature
2021-05-06 04:16:26 INFO::Writing residuals to file output2/residuals.rds
2021-05-06 04:16:27 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2021-05-06 04:16:27 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 ]
> 
> 
> proc.time()
   user  system elapsed 
  42.51    0.39   42.89

Maaslin2.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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"
2021-05-06 04:16:29 INFO::Writing function arguments to log file
2021-05-06 04:16:29 INFO::Verifying options selected are valid
2021-05-06 04:16:29 INFO::Determining format of input files
2021-05-06 04:16:29 INFO::Input format is data samples as rows and metadata samples as rows
2021-05-06 04:16:29 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-05-06 04:16:29 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2021-05-06 04:16:29 INFO::Filter data based on min abundance and min prevalence
2021-05-06 04:16:29 INFO::Total samples in data: 1595
2021-05-06 04:16:29 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-05-06 04:16:29 INFO::Total filtered features: 0
2021-05-06 04:16:29 INFO::Filtered feature names from abundance and prevalence filtering:
2021-05-06 04:16:29 INFO::Running selected normalization method: TSS
2021-05-06 04:16:31 INFO::Total filtered features with variance filtering: 0
2021-05-06 04:16:31 INFO::Filtered feature names from variance filtering:
2021-05-06 04:16:31 INFO::Bypass z-score application to metadata
2021-05-06 04:16:31 INFO::Running selected transform method: AST
2021-05-06 04:16:31 INFO::Running selected analysis method: LM
2021-05-06 04:16:31 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-05-06 04:16:33 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-05-06 04:16:33 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-05-06 04:16:33 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-05-06 04:16:33 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-05-06 04:16:34 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-05-06 04:16:34 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-05-06 04:16:34 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-05-06 04:16:34 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-05-06 04:16:34 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-05-06 04:16:35 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-05-06 04:16:35 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-05-06 04:16:35 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-05-06 04:16:35 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-05-06 04:16:35 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-05-06 04:16:36 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-05-06 04:16:36 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-05-06 04:16:36 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-05-06 04:16:36 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-05-06 04:16:36 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-05-06 04:16:37 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-05-06 04:16:37 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-05-06 04:16:37 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-05-06 04:16:37 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-05-06 04:16:37 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-05-06 04:16:38 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-05-06 04:16:38 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-05-06 04:16:38 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-05-06 04:16:38 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-05-06 04:16:38 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-05-06 04:16:39 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-05-06 04:16:39 INFO::Fitting model to feature number 32, Prevotella.copri
2021-05-06 04:16:39 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-05-06 04:16:39 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-05-06 04:16:39 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-05-06 04:16:40 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-05-06 04:16:40 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-05-06 04:16:40 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-05-06 04:16:40 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-05-06 04:16:40 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-05-06 04:16:40 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-05-06 04:16:41 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-05-06 04:16:41 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-05-06 04:16:41 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-05-06 04:16:41 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-05-06 04:16:41 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-05-06 04:16:42 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-05-06 04:16:42 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-05-06 04:16:42 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-05-06 04:16:42 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-05-06 04:16:42 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-05-06 04:16:43 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-05-06 04:16:43 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-05-06 04:16:43 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-05-06 04:16:43 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-05-06 04:16:43 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-05-06 04:16:44 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-05-06 04:16:44 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-05-06 04:16:44 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-05-06 04:16:44 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-05-06 04:16:44 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-05-06 04:16:44 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-05-06 04:16:45 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-05-06 04:16:45 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-05-06 04:16:45 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-05-06 04:16:45 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-05-06 04:16:46 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-05-06 04:16:46 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-05-06 04:16:46 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-05-06 04:16:46 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-05-06 04:16:47 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-05-06 04:16:47 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-05-06 04:16:47 INFO::Fitting model to feature number 73, Dialister.invisus
2021-05-06 04:16:47 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-05-06 04:16:47 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-05-06 04:16:47 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-05-06 04:16:48 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-05-06 04:16:48 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-05-06 04:16:48 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-05-06 04:16:48 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-05-06 04:16:48 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-05-06 04:16:48 INFO::Fitting model to feature number 82, Escherichia.coli
2021-05-06 04:16:49 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-05-06 04:16:49 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-05-06 04:16:49 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-05-06 04:16:49 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-05-06 04:16:50 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-05-06 04:16:50 INFO::Counting total values for each feature
2021-05-06 04:16:50 INFO::Writing residuals to file output/residuals.rds
2021-05-06 04:16:50 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2021-05-06 04:16:50 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): output/significant_results.tsv
[1] "Creating output folder"
2021-05-06 04:16:50 INFO::Writing function arguments to log file
2021-05-06 04:16:50 INFO::Verifying options selected are valid
2021-05-06 04:16:50 INFO::Determining format of input files
2021-05-06 04:16:50 INFO::Input format is data samples as rows and metadata samples as rows
2021-05-06 04:16:50 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-05-06 04:16:50 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2021-05-06 04:16:50 INFO::Filter data based on min abundance and min prevalence
2021-05-06 04:16:50 INFO::Total samples in data: 1595
2021-05-06 04:16:50 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-05-06 04:16:50 INFO::Total filtered features: 0
2021-05-06 04:16:50 INFO::Filtered feature names from abundance and prevalence filtering:
2021-05-06 04:16:50 INFO::Running selected normalization method: NONE
2021-05-06 04:16:50 INFO::Total filtered features with variance filtering: 0
2021-05-06 04:16:50 INFO::Filtered feature names from variance filtering:
2021-05-06 04:16:50 INFO::Bypass z-score application to metadata
2021-05-06 04:16:50 INFO::Running selected transform method: AST
2021-05-06 04:16:50 INFO::Running selected analysis method: LM
2021-05-06 04:16:50 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-05-06 04:16:50 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-05-06 04:16:51 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-05-06 04:16:51 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-05-06 04:16:51 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-05-06 04:16:51 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-05-06 04:16:51 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-05-06 04:16:52 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-05-06 04:16:52 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-05-06 04:16:52 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-05-06 04:16:52 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-05-06 04:16:52 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-05-06 04:16:53 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-05-06 04:16:53 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-05-06 04:16:53 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-05-06 04:16:53 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-05-06 04:16:54 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-05-06 04:16:54 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-05-06 04:16:54 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-05-06 04:16:54 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-05-06 04:16:54 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-05-06 04:16:55 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-05-06 04:16:55 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-05-06 04:16:55 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-05-06 04:16:55 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-05-06 04:16:55 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-05-06 04:16:56 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-05-06 04:16:56 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-05-06 04:16:56 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-05-06 04:16:56 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-05-06 04:16:56 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-05-06 04:16:56 INFO::Fitting model to feature number 32, Prevotella.copri
2021-05-06 04:16:57 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-05-06 04:16:57 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-05-06 04:16:57 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-05-06 04:16:57 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-05-06 04:16:57 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-05-06 04:16:58 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-05-06 04:16:58 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-05-06 04:16:58 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-05-06 04:16:58 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-05-06 04:16:58 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-05-06 04:16:58 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-05-06 04:16:59 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-05-06 04:16:59 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-05-06 04:16:59 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-05-06 04:16:59 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-05-06 04:17:00 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-05-06 04:17:00 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-05-06 04:17:00 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-05-06 04:17:00 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-05-06 04:17:01 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-05-06 04:17:01 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-05-06 04:17:01 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-05-06 04:17:01 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-05-06 04:17:01 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-05-06 04:17:02 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-05-06 04:17:02 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-05-06 04:17:02 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-05-06 04:17:02 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-05-06 04:17:02 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-05-06 04:17:02 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-05-06 04:17:03 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-05-06 04:17:03 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-05-06 04:17:03 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-05-06 04:17:03 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-05-06 04:17:03 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-05-06 04:17:03 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-05-06 04:17:03 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-05-06 04:17:04 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-05-06 04:17:04 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-05-06 04:17:04 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-05-06 04:17:04 INFO::Fitting model to feature number 73, Dialister.invisus
2021-05-06 04:17:04 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-05-06 04:17:04 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-05-06 04:17:05 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-05-06 04:17:05 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-05-06 04:17:05 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-05-06 04:17:05 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-05-06 04:17:05 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-05-06 04:17:05 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-05-06 04:17:06 INFO::Fitting model to feature number 82, Escherichia.coli
2021-05-06 04:17:06 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-05-06 04:17:06 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-05-06 04:17:06 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-05-06 04:17:06 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-05-06 04:17:06 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-05-06 04:17:07 INFO::Counting total values for each feature
2021-05-06 04:17:07 INFO::Writing residuals to file output2/residuals.rds
2021-05-06 04:17:07 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2021-05-06 04:17:07 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 ]
> 
> 
> proc.time()
   user  system elapsed 
  39.48    0.37   39.89

Example timings

Maaslin2.Rcheck/examples_i386/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2100.05 5.13105.70

Maaslin2.Rcheck/examples_x64/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2105.20 4.71110.06