Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:06:29 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 tokay2


To the developers/maintainers of the Maaslin2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1026/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.8.0  (landing page)
Lauren McIver
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_14
git_last_commit: 6e36871
git_last_commit_date: 2021-10-26 12:53:13 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Maaslin2
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Maaslin2_1.8.0.tar.gz
StartedAt: 2022-01-23 21:46:09 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 21:51:00 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 291.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Maaslin2_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Maaslin2.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.8.0'
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
Maaslin2   80   4.73    85.4
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
Maaslin2 79.15   3.67    82.9
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.



Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Maaslin2_1.8.0.tar.gz && rm -rf Maaslin2.buildbin-libdir && mkdir Maaslin2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Maaslin2.buildbin-libdir Maaslin2_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Maaslin2_1.8.0.zip && rm Maaslin2_1.8.0.tar.gz Maaslin2_1.8.0.zip
###
##############################################################################
##############################################################################


  % 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  323k  100  323k    0     0  1419k      0 --:--:-- --:--:-- --:--:-- 1425k

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 1.3.4
Current Matrix version is 1.4.0
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_1.8.0.zip
* DONE (Maaslin2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Maaslin2' successfully unpacked and MD5 sums checked

Tests output

Maaslin2.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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"
2022-01-23 21:49:46 INFO::Writing function arguments to log file
2022-01-23 21:49:47 INFO::Verifying options selected are valid
2022-01-23 21:49:47 INFO::Determining format of input files
2022-01-23 21:49:47 INFO::Input format is data samples as rows and metadata samples as rows
2022-01-23 21:49:47 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2022-01-23 21:49:47 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2022-01-23 21:49:47 INFO::Filter data based on min abundance and min prevalence
2022-01-23 21:49:47 INFO::Total samples in data: 1595
2022-01-23 21:49:47 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2022-01-23 21:49:47 INFO::Total filtered features: 0
2022-01-23 21:49:47 INFO::Filtered feature names from abundance and prevalence filtering:
2022-01-23 21:49:47 INFO::Total filtered features with variance filtering: 0
2022-01-23 21:49:47 INFO::Filtered feature names from variance filtering:
2022-01-23 21:49:47 INFO::Running selected normalization method: TSS
2022-01-23 21:49:48 INFO::Bypass z-score application to metadata
2022-01-23 21:49:48 INFO::Running selected transform method: AST
2022-01-23 21:49:48 INFO::Running selected analysis method: LM
2022-01-23 21:49:48 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2022-01-23 21:49:49 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2022-01-23 21:49:49 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2022-01-23 21:49:49 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2022-01-23 21:49:49 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2022-01-23 21:49:49 INFO::Fitting model to feature number 6, Bacteroides.caccae
2022-01-23 21:49:50 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2022-01-23 21:49:50 INFO::Fitting model to feature number 8, Bacteroides.dorei
2022-01-23 21:49:50 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2022-01-23 21:49:50 INFO::Fitting model to feature number 10, Bacteroides.faecis
2022-01-23 21:49:50 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2022-01-23 21:49:50 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2022-01-23 21:49:51 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2022-01-23 21:49:51 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2022-01-23 21:49:51 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2022-01-23 21:49:51 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2022-01-23 21:49:51 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2022-01-23 21:49:51 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2022-01-23 21:49:52 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2022-01-23 21:49:52 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2022-01-23 21:49:52 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2022-01-23 21:49:52 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2022-01-23 21:49:52 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2022-01-23 21:49:52 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2022-01-23 21:49:53 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2022-01-23 21:49:53 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2022-01-23 21:49:53 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2022-01-23 21:49:53 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2022-01-23 21:49:53 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2022-01-23 21:49:53 INFO::Fitting model to feature number 30, Paraprevotella.clara
2022-01-23 21:49:54 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2022-01-23 21:49:54 INFO::Fitting model to feature number 32, Prevotella.copri
2022-01-23 21:49:54 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2022-01-23 21:49:54 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2022-01-23 21:49:54 INFO::Fitting model to feature number 35, Alistipes.putredinis
2022-01-23 21:49:54 INFO::Fitting model to feature number 36, Alistipes.shahii
2022-01-23 21:49:55 INFO::Fitting model to feature number 37, Alistipes.unclassified
2022-01-23 21:49:55 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2022-01-23 21:49:55 INFO::Fitting model to feature number 39, Clostridium.bolteae
2022-01-23 21:49:55 INFO::Fitting model to feature number 40, Clostridium.citroniae
2022-01-23 21:49:55 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2022-01-23 21:49:55 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2022-01-23 21:49:55 INFO::Fitting model to feature number 43, Clostridium.leptum
2022-01-23 21:49:56 INFO::Fitting model to feature number 44, Clostridium.nexile
2022-01-23 21:49:56 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2022-01-23 21:49:56 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2022-01-23 21:49:56 INFO::Fitting model to feature number 47, Eubacterium.eligens
2022-01-23 21:49:56 INFO::Fitting model to feature number 48, Eubacterium.hallii
2022-01-23 21:49:56 INFO::Fitting model to feature number 49, Eubacterium.rectale
2022-01-23 21:49:57 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2022-01-23 21:49:57 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2022-01-23 21:49:57 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2022-01-23 21:49:57 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2022-01-23 21:49:57 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2022-01-23 21:49:58 INFO::Fitting model to feature number 55, Ruminococcus.torques
2022-01-23 21:49:58 INFO::Fitting model to feature number 56, Coprococcus.comes
2022-01-23 21:49:58 INFO::Fitting model to feature number 57, Dorea.longicatena
2022-01-23 21:49:58 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2022-01-23 21:49:58 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2022-01-23 21:49:58 INFO::Fitting model to feature number 60, Roseburia.hominis
2022-01-23 21:49:58 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2022-01-23 21:49:59 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2022-01-23 21:49:59 INFO::Fitting model to feature number 63, Roseburia.unclassified
2022-01-23 21:49:59 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2022-01-23 21:49:59 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2022-01-23 21:49:59 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2022-01-23 21:49:59 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2022-01-23 21:50:00 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2022-01-23 21:50:00 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2022-01-23 21:50:00 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2022-01-23 21:50:00 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2022-01-23 21:50:00 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2022-01-23 21:50:00 INFO::Fitting model to feature number 73, Dialister.invisus
2022-01-23 21:50:01 INFO::Fitting model to feature number 74, Veillonella.atypica
2022-01-23 21:50:01 INFO::Fitting model to feature number 75, Veillonella.dispar
2022-01-23 21:50:01 INFO::Fitting model to feature number 76, Veillonella.parvula
2022-01-23 21:50:01 INFO::Fitting model to feature number 77, Veillonella.unclassified
2022-01-23 21:50:01 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2022-01-23 21:50:01 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2022-01-23 21:50:02 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2022-01-23 21:50:02 INFO::Fitting model to feature number 81, Bilophila.unclassified
2022-01-23 21:50:02 INFO::Fitting model to feature number 82, Escherichia.coli
2022-01-23 21:50:02 INFO::Fitting model to feature number 83, Escherichia.unclassified
2022-01-23 21:50:02 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2022-01-23 21:50:02 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2022-01-23 21:50:02 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2022-01-23 21:50:03 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2022-01-23 21:50:03 INFO::Counting total values for each feature
2022-01-23 21:50:03 INFO::Writing residuals to file output/residuals.rds
2022-01-23 21:50:03 INFO::Writing fitted values to file output/fitted.rds
2022-01-23 21:50:03 INFO::Writing extracted random effects to file output/ranef.rds
2022-01-23 21:50:03 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2022-01-23 21:50:03 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"
2022-01-23 21:50:03 INFO::Writing function arguments to log file
2022-01-23 21:50:03 INFO::Verifying options selected are valid
2022-01-23 21:50:03 INFO::Determining format of input files
2022-01-23 21:50:03 INFO::Input format is data samples as rows and metadata samples as rows
2022-01-23 21:50:03 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2022-01-23 21:50:03 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2022-01-23 21:50:03 INFO::Filter data based on min abundance and min prevalence
2022-01-23 21:50:03 INFO::Total samples in data: 1595
2022-01-23 21:50:03 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2022-01-23 21:50:03 INFO::Total filtered features: 0
2022-01-23 21:50:03 INFO::Filtered feature names from abundance and prevalence filtering:
2022-01-23 21:50:03 INFO::Total filtered features with variance filtering: 0
2022-01-23 21:50:03 INFO::Filtered feature names from variance filtering:
2022-01-23 21:50:03 INFO::Running selected normalization method: NONE
2022-01-23 21:50:03 INFO::Bypass z-score application to metadata
2022-01-23 21:50:03 INFO::Running selected transform method: AST
2022-01-23 21:50:03 INFO::Running selected analysis method: LM
2022-01-23 21:50:03 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2022-01-23 21:50:03 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2022-01-23 21:50:03 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2022-01-23 21:50:03 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2022-01-23 21:50:04 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2022-01-23 21:50:04 INFO::Fitting model to feature number 6, Bacteroides.caccae
2022-01-23 21:50:04 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2022-01-23 21:50:04 INFO::Fitting model to feature number 8, Bacteroides.dorei
2022-01-23 21:50:04 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2022-01-23 21:50:04 INFO::Fitting model to feature number 10, Bacteroides.faecis
2022-01-23 21:50:05 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2022-01-23 21:50:05 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2022-01-23 21:50:05 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2022-01-23 21:50:05 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2022-01-23 21:50:05 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2022-01-23 21:50:05 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2022-01-23 21:50:05 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2022-01-23 21:50:06 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2022-01-23 21:50:06 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2022-01-23 21:50:06 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2022-01-23 21:50:06 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2022-01-23 21:50:06 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2022-01-23 21:50:06 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2022-01-23 21:50:07 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2022-01-23 21:50:07 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2022-01-23 21:50:07 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2022-01-23 21:50:07 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2022-01-23 21:50:07 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2022-01-23 21:50:07 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2022-01-23 21:50:08 INFO::Fitting model to feature number 30, Paraprevotella.clara
2022-01-23 21:50:08 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2022-01-23 21:50:08 INFO::Fitting model to feature number 32, Prevotella.copri
2022-01-23 21:50:08 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2022-01-23 21:50:08 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2022-01-23 21:50:08 INFO::Fitting model to feature number 35, Alistipes.putredinis
2022-01-23 21:50:09 INFO::Fitting model to feature number 36, Alistipes.shahii
2022-01-23 21:50:09 INFO::Fitting model to feature number 37, Alistipes.unclassified
2022-01-23 21:50:09 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2022-01-23 21:50:09 INFO::Fitting model to feature number 39, Clostridium.bolteae
2022-01-23 21:50:09 INFO::Fitting model to feature number 40, Clostridium.citroniae
2022-01-23 21:50:10 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2022-01-23 21:50:10 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2022-01-23 21:50:10 INFO::Fitting model to feature number 43, Clostridium.leptum
2022-01-23 21:50:10 INFO::Fitting model to feature number 44, Clostridium.nexile
2022-01-23 21:50:10 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2022-01-23 21:50:10 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2022-01-23 21:50:10 INFO::Fitting model to feature number 47, Eubacterium.eligens
2022-01-23 21:50:11 INFO::Fitting model to feature number 48, Eubacterium.hallii
2022-01-23 21:50:11 INFO::Fitting model to feature number 49, Eubacterium.rectale
2022-01-23 21:50:11 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2022-01-23 21:50:11 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2022-01-23 21:50:11 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2022-01-23 21:50:11 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2022-01-23 21:50:11 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2022-01-23 21:50:12 INFO::Fitting model to feature number 55, Ruminococcus.torques
2022-01-23 21:50:12 INFO::Fitting model to feature number 56, Coprococcus.comes
2022-01-23 21:50:12 INFO::Fitting model to feature number 57, Dorea.longicatena
2022-01-23 21:50:12 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2022-01-23 21:50:12 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2022-01-23 21:50:13 INFO::Fitting model to feature number 60, Roseburia.hominis
2022-01-23 21:50:13 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2022-01-23 21:50:13 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2022-01-23 21:50:13 INFO::Fitting model to feature number 63, Roseburia.unclassified
2022-01-23 21:50:13 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2022-01-23 21:50:13 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2022-01-23 21:50:13 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2022-01-23 21:50:14 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2022-01-23 21:50:14 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2022-01-23 21:50:14 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2022-01-23 21:50:14 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2022-01-23 21:50:14 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2022-01-23 21:50:14 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2022-01-23 21:50:15 INFO::Fitting model to feature number 73, Dialister.invisus
2022-01-23 21:50:15 INFO::Fitting model to feature number 74, Veillonella.atypica
2022-01-23 21:50:15 INFO::Fitting model to feature number 75, Veillonella.dispar
2022-01-23 21:50:15 INFO::Fitting model to feature number 76, Veillonella.parvula
2022-01-23 21:50:15 INFO::Fitting model to feature number 77, Veillonella.unclassified
2022-01-23 21:50:16 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2022-01-23 21:50:16 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2022-01-23 21:50:16 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2022-01-23 21:50:16 INFO::Fitting model to feature number 81, Bilophila.unclassified
2022-01-23 21:50:16 INFO::Fitting model to feature number 82, Escherichia.coli
2022-01-23 21:50:17 INFO::Fitting model to feature number 83, Escherichia.unclassified
2022-01-23 21:50:17 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2022-01-23 21:50:17 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2022-01-23 21:50:17 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2022-01-23 21:50:17 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2022-01-23 21:50:17 INFO::Counting total values for each feature
2022-01-23 21:50:17 INFO::Writing residuals to file output2/residuals.rds
2022-01-23 21:50:17 INFO::Writing fitted values to file output2/fitted.rds
2022-01-23 21:50:18 INFO::Writing extracted random effects to file output2/ranef.rds
2022-01-23 21:50:18 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2022-01-23 21:50:18 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  32.00    0.57   32.57 

Maaslin2.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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"
2022-01-23 21:50:20 INFO::Writing function arguments to log file
2022-01-23 21:50:20 INFO::Verifying options selected are valid
2022-01-23 21:50:20 INFO::Determining format of input files
2022-01-23 21:50:20 INFO::Input format is data samples as rows and metadata samples as rows
2022-01-23 21:50:20 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2022-01-23 21:50:20 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2022-01-23 21:50:20 INFO::Filter data based on min abundance and min prevalence
2022-01-23 21:50:20 INFO::Total samples in data: 1595
2022-01-23 21:50:20 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2022-01-23 21:50:20 INFO::Total filtered features: 0
2022-01-23 21:50:20 INFO::Filtered feature names from abundance and prevalence filtering:
2022-01-23 21:50:20 INFO::Total filtered features with variance filtering: 0
2022-01-23 21:50:20 INFO::Filtered feature names from variance filtering:
2022-01-23 21:50:20 INFO::Running selected normalization method: TSS
2022-01-23 21:50:21 INFO::Bypass z-score application to metadata
2022-01-23 21:50:21 INFO::Running selected transform method: AST
2022-01-23 21:50:21 INFO::Running selected analysis method: LM
2022-01-23 21:50:21 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2022-01-23 21:50:22 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2022-01-23 21:50:22 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2022-01-23 21:50:22 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2022-01-23 21:50:22 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2022-01-23 21:50:23 INFO::Fitting model to feature number 6, Bacteroides.caccae
2022-01-23 21:50:23 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2022-01-23 21:50:23 INFO::Fitting model to feature number 8, Bacteroides.dorei
2022-01-23 21:50:23 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2022-01-23 21:50:23 INFO::Fitting model to feature number 10, Bacteroides.faecis
2022-01-23 21:50:23 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2022-01-23 21:50:24 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2022-01-23 21:50:24 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2022-01-23 21:50:24 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2022-01-23 21:50:24 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2022-01-23 21:50:24 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2022-01-23 21:50:25 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2022-01-23 21:50:25 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2022-01-23 21:50:25 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2022-01-23 21:50:25 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2022-01-23 21:50:25 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2022-01-23 21:50:25 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2022-01-23 21:50:26 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2022-01-23 21:50:26 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2022-01-23 21:50:26 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2022-01-23 21:50:26 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2022-01-23 21:50:26 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2022-01-23 21:50:27 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2022-01-23 21:50:27 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2022-01-23 21:50:27 INFO::Fitting model to feature number 30, Paraprevotella.clara
2022-01-23 21:50:27 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2022-01-23 21:50:27 INFO::Fitting model to feature number 32, Prevotella.copri
2022-01-23 21:50:27 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2022-01-23 21:50:28 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2022-01-23 21:50:28 INFO::Fitting model to feature number 35, Alistipes.putredinis
2022-01-23 21:50:28 INFO::Fitting model to feature number 36, Alistipes.shahii
2022-01-23 21:50:28 INFO::Fitting model to feature number 37, Alistipes.unclassified
2022-01-23 21:50:28 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2022-01-23 21:50:28 INFO::Fitting model to feature number 39, Clostridium.bolteae
2022-01-23 21:50:29 INFO::Fitting model to feature number 40, Clostridium.citroniae
2022-01-23 21:50:29 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2022-01-23 21:50:29 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2022-01-23 21:50:29 INFO::Fitting model to feature number 43, Clostridium.leptum
2022-01-23 21:50:29 INFO::Fitting model to feature number 44, Clostridium.nexile
2022-01-23 21:50:29 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2022-01-23 21:50:30 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2022-01-23 21:50:30 INFO::Fitting model to feature number 47, Eubacterium.eligens
2022-01-23 21:50:30 INFO::Fitting model to feature number 48, Eubacterium.hallii
2022-01-23 21:50:30 INFO::Fitting model to feature number 49, Eubacterium.rectale
2022-01-23 21:50:30 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2022-01-23 21:50:30 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2022-01-23 21:50:31 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2022-01-23 21:50:31 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2022-01-23 21:50:31 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2022-01-23 21:50:31 INFO::Fitting model to feature number 55, Ruminococcus.torques
2022-01-23 21:50:32 INFO::Fitting model to feature number 56, Coprococcus.comes
2022-01-23 21:50:32 INFO::Fitting model to feature number 57, Dorea.longicatena
2022-01-23 21:50:32 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2022-01-23 21:50:32 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2022-01-23 21:50:32 INFO::Fitting model to feature number 60, Roseburia.hominis
2022-01-23 21:50:32 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2022-01-23 21:50:33 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2022-01-23 21:50:33 INFO::Fitting model to feature number 63, Roseburia.unclassified
2022-01-23 21:50:33 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2022-01-23 21:50:33 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2022-01-23 21:50:33 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2022-01-23 21:50:33 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2022-01-23 21:50:33 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2022-01-23 21:50:34 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2022-01-23 21:50:34 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2022-01-23 21:50:34 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2022-01-23 21:50:34 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2022-01-23 21:50:34 INFO::Fitting model to feature number 73, Dialister.invisus
2022-01-23 21:50:34 INFO::Fitting model to feature number 74, Veillonella.atypica
2022-01-23 21:50:35 INFO::Fitting model to feature number 75, Veillonella.dispar
2022-01-23 21:50:35 INFO::Fitting model to feature number 76, Veillonella.parvula
2022-01-23 21:50:35 INFO::Fitting model to feature number 77, Veillonella.unclassified
2022-01-23 21:50:35 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2022-01-23 21:50:35 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2022-01-23 21:50:35 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2022-01-23 21:50:36 INFO::Fitting model to feature number 81, Bilophila.unclassified
2022-01-23 21:50:36 INFO::Fitting model to feature number 82, Escherichia.coli
2022-01-23 21:50:36 INFO::Fitting model to feature number 83, Escherichia.unclassified
2022-01-23 21:50:36 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2022-01-23 21:50:36 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2022-01-23 21:50:36 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2022-01-23 21:50:37 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2022-01-23 21:50:37 INFO::Counting total values for each feature
2022-01-23 21:50:37 INFO::Writing residuals to file output/residuals.rds
2022-01-23 21:50:37 INFO::Writing fitted values to file output/fitted.rds
2022-01-23 21:50:37 INFO::Writing extracted random effects to file output/ranef.rds
2022-01-23 21:50:37 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2022-01-23 21:50:37 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"
2022-01-23 21:50:37 INFO::Writing function arguments to log file
2022-01-23 21:50:37 INFO::Verifying options selected are valid
2022-01-23 21:50:37 INFO::Determining format of input files
2022-01-23 21:50:37 INFO::Input format is data samples as rows and metadata samples as rows
2022-01-23 21:50:37 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2022-01-23 21:50:37 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2022-01-23 21:50:37 INFO::Filter data based on min abundance and min prevalence
2022-01-23 21:50:37 INFO::Total samples in data: 1595
2022-01-23 21:50:37 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2022-01-23 21:50:37 INFO::Total filtered features: 0
2022-01-23 21:50:37 INFO::Filtered feature names from abundance and prevalence filtering:
2022-01-23 21:50:37 INFO::Total filtered features with variance filtering: 0
2022-01-23 21:50:37 INFO::Filtered feature names from variance filtering:
2022-01-23 21:50:37 INFO::Running selected normalization method: NONE
2022-01-23 21:50:37 INFO::Bypass z-score application to metadata
2022-01-23 21:50:37 INFO::Running selected transform method: AST
2022-01-23 21:50:37 INFO::Running selected analysis method: LM
2022-01-23 21:50:37 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2022-01-23 21:50:37 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2022-01-23 21:50:37 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2022-01-23 21:50:38 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2022-01-23 21:50:38 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2022-01-23 21:50:38 INFO::Fitting model to feature number 6, Bacteroides.caccae
2022-01-23 21:50:38 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2022-01-23 21:50:38 INFO::Fitting model to feature number 8, Bacteroides.dorei
2022-01-23 21:50:38 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2022-01-23 21:50:39 INFO::Fitting model to feature number 10, Bacteroides.faecis
2022-01-23 21:50:39 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2022-01-23 21:50:39 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2022-01-23 21:50:39 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2022-01-23 21:50:39 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2022-01-23 21:50:39 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2022-01-23 21:50:40 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2022-01-23 21:50:40 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2022-01-23 21:50:40 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2022-01-23 21:50:40 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2022-01-23 21:50:40 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2022-01-23 21:50:41 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2022-01-23 21:50:41 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2022-01-23 21:50:41 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2022-01-23 21:50:41 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2022-01-23 21:50:41 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2022-01-23 21:50:41 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2022-01-23 21:50:42 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2022-01-23 21:50:42 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2022-01-23 21:50:42 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2022-01-23 21:50:42 INFO::Fitting model to feature number 30, Paraprevotella.clara
2022-01-23 21:50:42 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2022-01-23 21:50:42 INFO::Fitting model to feature number 32, Prevotella.copri
2022-01-23 21:50:43 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2022-01-23 21:50:43 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2022-01-23 21:50:43 INFO::Fitting model to feature number 35, Alistipes.putredinis
2022-01-23 21:50:43 INFO::Fitting model to feature number 36, Alistipes.shahii
2022-01-23 21:50:43 INFO::Fitting model to feature number 37, Alistipes.unclassified
2022-01-23 21:50:44 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2022-01-23 21:50:44 INFO::Fitting model to feature number 39, Clostridium.bolteae
2022-01-23 21:50:44 INFO::Fitting model to feature number 40, Clostridium.citroniae
2022-01-23 21:50:44 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2022-01-23 21:50:44 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2022-01-23 21:50:44 INFO::Fitting model to feature number 43, Clostridium.leptum
2022-01-23 21:50:44 INFO::Fitting model to feature number 44, Clostridium.nexile
2022-01-23 21:50:45 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2022-01-23 21:50:45 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2022-01-23 21:50:45 INFO::Fitting model to feature number 47, Eubacterium.eligens
2022-01-23 21:50:45 INFO::Fitting model to feature number 48, Eubacterium.hallii
2022-01-23 21:50:45 INFO::Fitting model to feature number 49, Eubacterium.rectale
2022-01-23 21:50:45 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2022-01-23 21:50:46 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2022-01-23 21:50:46 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2022-01-23 21:50:46 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2022-01-23 21:50:46 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2022-01-23 21:50:46 INFO::Fitting model to feature number 55, Ruminococcus.torques
2022-01-23 21:50:46 INFO::Fitting model to feature number 56, Coprococcus.comes
2022-01-23 21:50:47 INFO::Fitting model to feature number 57, Dorea.longicatena
2022-01-23 21:50:47 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2022-01-23 21:50:47 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2022-01-23 21:50:47 INFO::Fitting model to feature number 60, Roseburia.hominis
2022-01-23 21:50:47 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2022-01-23 21:50:47 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2022-01-23 21:50:48 INFO::Fitting model to feature number 63, Roseburia.unclassified
2022-01-23 21:50:48 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2022-01-23 21:50:48 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2022-01-23 21:50:48 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2022-01-23 21:50:48 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2022-01-23 21:50:48 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2022-01-23 21:50:49 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2022-01-23 21:50:49 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2022-01-23 21:50:49 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2022-01-23 21:50:49 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2022-01-23 21:50:49 INFO::Fitting model to feature number 73, Dialister.invisus
2022-01-23 21:50:50 INFO::Fitting model to feature number 74, Veillonella.atypica
2022-01-23 21:50:50 INFO::Fitting model to feature number 75, Veillonella.dispar
2022-01-23 21:50:50 INFO::Fitting model to feature number 76, Veillonella.parvula
2022-01-23 21:50:50 INFO::Fitting model to feature number 77, Veillonella.unclassified
2022-01-23 21:50:50 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2022-01-23 21:50:50 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2022-01-23 21:50:51 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2022-01-23 21:50:51 INFO::Fitting model to feature number 81, Bilophila.unclassified
2022-01-23 21:50:51 INFO::Fitting model to feature number 82, Escherichia.coli
2022-01-23 21:50:51 INFO::Fitting model to feature number 83, Escherichia.unclassified
2022-01-23 21:50:51 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2022-01-23 21:50:51 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2022-01-23 21:50:52 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2022-01-23 21:50:52 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2022-01-23 21:50:52 INFO::Counting total values for each feature
2022-01-23 21:50:52 INFO::Writing residuals to file output2/residuals.rds
2022-01-23 21:50:52 INFO::Writing fitted values to file output2/fitted.rds
2022-01-23 21:50:52 INFO::Writing extracted random effects to file output2/ranef.rds
2022-01-23 21:50:52 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2022-01-23 21:50:52 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 
  34.00    0.32   34.34 

Example timings

Maaslin2.Rcheck/examples_i386/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin280.00 4.7385.40

Maaslin2.Rcheck/examples_x64/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin279.15 3.6782.90