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CHECK report for Maaslin2 on tokay1

This page was generated on 2020-04-15 12:32:51 -0400 (Wed, 15 Apr 2020).

Package 935/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.0.0
Lauren McIver
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Maaslin2
Branch: RELEASE_3_10
Last Commit: f70c81e
Last Changed Date: 2019-10-29 13:11:48 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: Maaslin2
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Maaslin2_1.0.0.tar.gz
StartedAt: 2020-04-15 04:24:04 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:29:24 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 320.1 seconds
RetCode: 1
Status:  ERROR  
CheckDir: Maaslin2.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Maaslin2_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Maaslin2.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Maaslin2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Maaslin2 95.94   0.69   98.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Maaslin2 79.95   0.64   81.82
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2020-04-15 04:28:35 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
  2020-04-15 04:28:36 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
  2020-04-15 04:28:36 INFO::Fitting model to feature number 87, C2likevirus.unclassified
  2020-04-15 04:28:36 INFO::Counting total values for each feature
  2020-04-15 04:28:36 INFO::Writing residuals to file output2/residuals.rds
  2020-04-15 04:28:37 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
  2020-04-15 04:28:37 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): output2/significant_results.tsv
  == testthat results  ===========================================================
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 3 ]
  1. Failure: (unknown) (@test_Maaslin2.R#17) 
  2. Failure: (unknown) (@test_Maaslin2.R#18) 
  3. Failure: (unknown) (@test_Maaslin2.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2020-04-15 04:29:19 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
  2020-04-15 04:29:20 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
  2020-04-15 04:29:20 INFO::Fitting model to feature number 87, C2likevirus.unclassified
  2020-04-15 04:29:20 INFO::Counting total values for each feature
  2020-04-15 04:29:20 INFO::Writing residuals to file output2/residuals.rds
  2020-04-15 04:29:20 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
  2020-04-15 04:29:20 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
  == testthat results  ===========================================================
  [ OK: 9 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 3 ]
  1. Failure: (unknown) (@test_Maaslin2.R#17) 
  2. Failure: (unknown) (@test_Maaslin2.R#18) 
  3. Failure: (unknown) (@test_Maaslin2.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.10-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 https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Maaslin2_1.0.0.tar.gz && rm -rf Maaslin2.buildbin-libdir && mkdir Maaslin2.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Maaslin2.buildbin-libdir Maaslin2_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Maaslin2_1.0.0.zip && rm Maaslin2_1.0.0.tar.gz Maaslin2_1.0.0.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  318k  100  318k    0     0  2628k      0 --:--:-- --:--:-- --:--:-- 2718k

install for i386

* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Maaslin2'
    finding HTML links ... done
    Maaslin2                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Maaslin2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Maaslin2' as Maaslin2_1.0.0.zip
* DONE (Maaslin2)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Maaslin2' successfully unpacked and MD5 sums checked

Tests output

Maaslin2.Rcheck/tests_i386/testthat.Rout.fail


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
2020-04-15 04:27:48 INFO::Writing function arguments to log file
2020-04-15 04:27:48 INFO::Verifying options selected are valid
2020-04-15 04:27:48 INFO::Determining format of input files
2020-04-15 04:27:48 INFO::Input format is data samples as rows and metadata samples as rows
2020-04-15 04:27:48 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-04-15 04:27:48 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2020-04-15 04:27:48 INFO::Running selected normalization method: TSS
2020-04-15 04:27:49 INFO::Filter data based on min abundance and min prevalence
2020-04-15 04:27:49 INFO::Total samples in data: 1595
2020-04-15 04:27:49 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-04-15 04:27:49 INFO::Total filtered features: 0
2020-04-15 04:27:49 INFO::Filtered feature names:
2020-04-15 04:27:49 INFO::Bypass z-score application to metadata
2020-04-15 04:27:49 INFO::Running selected transform method: AST
2020-04-15 04:27:49 INFO::Running selected analysis method: LM
2020-04-15 04:27:50 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-04-15 04:27:51 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-04-15 04:27:51 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-04-15 04:27:51 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-04-15 04:27:52 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-04-15 04:27:52 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-04-15 04:27:52 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-04-15 04:27:52 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-04-15 04:27:53 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-04-15 04:27:53 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-04-15 04:27:53 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-04-15 04:27:54 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-04-15 04:27:54 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-04-15 04:27:54 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-04-15 04:27:54 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-04-15 04:27:55 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-04-15 04:27:55 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-04-15 04:27:55 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-04-15 04:27:56 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-04-15 04:27:56 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-04-15 04:27:56 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-04-15 04:27:56 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-04-15 04:27:57 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-04-15 04:27:57 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-04-15 04:27:57 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-04-15 04:27:58 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-04-15 04:27:58 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-04-15 04:27:58 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-04-15 04:27:58 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-04-15 04:27:59 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-04-15 04:27:59 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-04-15 04:27:59 INFO::Fitting model to feature number 32, Prevotella.copri
2020-04-15 04:28:00 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-04-15 04:28:00 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-04-15 04:28:00 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-04-15 04:28:00 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-04-15 04:28:01 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-04-15 04:28:01 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-04-15 04:28:01 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-04-15 04:28:01 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-04-15 04:28:02 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-04-15 04:28:02 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-04-15 04:28:02 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-04-15 04:28:02 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-04-15 04:28:03 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-04-15 04:28:03 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-04-15 04:28:03 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-04-15 04:28:03 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-04-15 04:28:04 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-04-15 04:28:04 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-04-15 04:28:04 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-04-15 04:28:04 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-04-15 04:28:05 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-04-15 04:28:05 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-04-15 04:28:05 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-04-15 04:28:06 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-04-15 04:28:06 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-04-15 04:28:06 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-04-15 04:28:07 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-04-15 04:28:07 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-04-15 04:28:07 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-04-15 04:28:08 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-04-15 04:28:08 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-04-15 04:28:08 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-04-15 04:28:08 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-04-15 04:28:09 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-04-15 04:28:09 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-04-15 04:28:09 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-04-15 04:28:09 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-04-15 04:28:10 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-04-15 04:28:10 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-04-15 04:28:10 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-04-15 04:28:11 INFO::Fitting model to feature number 73, Dialister.invisus
2020-04-15 04:28:11 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-04-15 04:28:11 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-04-15 04:28:11 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-04-15 04:28:12 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-04-15 04:28:12 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-04-15 04:28:12 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-04-15 04:28:13 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-04-15 04:28:13 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-04-15 04:28:13 INFO::Fitting model to feature number 82, Escherichia.coli
2020-04-15 04:28:13 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-04-15 04:28:14 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-04-15 04:28:14 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-04-15 04:28:14 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-04-15 04:28:14 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-04-15 04:28:15 INFO::Counting total values for each feature
2020-04-15 04:28:15 INFO::Writing residuals to file output/residuals.rds
2020-04-15 04:28:15 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2020-04-15 04:28:15 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. Failure: (unknown) (@test_Maaslin2.R#17)  --------------------------------
`x` not equal to `expected`.
5/208 mismatches
x[133]: "dysbiosisUC"
y[133]: "diagnosis"

x[134]: "dysbiosisnonIBD"
y[134]: "dysbiosisUC"

x[135]: "diagnosis"
y[135]: "dysbiosisnonIBD"

x[185]: "antibiotics"
y[185]: "diagnosis"

x[187]: "diagnosis"
y[187]: "antibiotics"

-- 2. Failure: (unknown) (@test_Maaslin2.R#18)  --------------------------------
`x` not equal to `expected`.
10/208 mismatches
x[133]: "Clostridium.nexile"
y[133]: "Ruminococcus.callidus"

x[134]: "Lachnospiraceae.bacterium.3.1.46FAA"
y[134]: "Clostridium.nexile"

x[135]: "Ruminococcus.callidus"
y[135]: "Lachnospiraceae.bacterium.3.1.46FAA"

x[185]: "Veillonella.parvula"
y[185]: "Ruminococcus.gnavus"

x[186]: "Ruminococcus.gnavus"
y[186]: "Ruminococcus.obeum"

-- 3. Failure: (unknown) (@test_Maaslin2.R#20)  --------------------------------
`x` not equal to `expected`.
10/208 mismatches (average diff: 427)
[133]  273 -  323 ==  -50
[134]  992 -  273 ==  719
[135]  323 -  992 == -669
[185]  853 -  970 == -117
[186]  970 - 1346 == -376
[187] 1346 - 1514 == -168
[188] 1514 -  415 == 1099
[189]  415 -  853 == -438
[203]  730 -  415 ==  315
...

[1] "Creating output folder"
2020-04-15 04:28:15 INFO::Writing function arguments to log file
2020-04-15 04:28:15 INFO::Verifying options selected are valid
2020-04-15 04:28:15 INFO::Determining format of input files
2020-04-15 04:28:15 INFO::Input format is data samples as rows and metadata samples as rows
2020-04-15 04:28:15 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-04-15 04:28:15 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2020-04-15 04:28:15 INFO::Running selected normalization method: NONE
2020-04-15 04:28:15 INFO::Filter data based on min abundance and min prevalence
2020-04-15 04:28:15 INFO::Total samples in data: 1595
2020-04-15 04:28:15 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-04-15 04:28:15 INFO::Total filtered features: 0
2020-04-15 04:28:15 INFO::Filtered feature names:
2020-04-15 04:28:15 INFO::Bypass z-score application to metadata
2020-04-15 04:28:15 INFO::Running selected transform method: AST
2020-04-15 04:28:15 INFO::Running selected analysis method: LM
2020-04-15 04:28:15 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-04-15 04:28:15 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-04-15 04:28:16 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-04-15 04:28:16 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-04-15 04:28:16 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-04-15 04:28:17 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-04-15 04:28:17 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-04-15 04:28:17 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-04-15 04:28:17 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-04-15 04:28:18 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-04-15 04:28:18 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-04-15 04:28:18 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-04-15 04:28:18 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-04-15 04:28:19 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-04-15 04:28:19 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-04-15 04:28:19 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-04-15 04:28:19 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-04-15 04:28:20 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-04-15 04:28:20 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-04-15 04:28:20 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-04-15 04:28:20 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-04-15 04:28:21 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-04-15 04:28:21 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-04-15 04:28:21 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-04-15 04:28:21 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-04-15 04:28:22 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-04-15 04:28:22 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-04-15 04:28:22 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-04-15 04:28:23 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-04-15 04:28:23 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-04-15 04:28:23 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-04-15 04:28:23 INFO::Fitting model to feature number 32, Prevotella.copri
2020-04-15 04:28:24 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-04-15 04:28:24 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-04-15 04:28:24 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-04-15 04:28:24 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-04-15 04:28:25 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-04-15 04:28:25 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-04-15 04:28:25 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-04-15 04:28:25 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-04-15 04:28:25 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-04-15 04:28:26 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-04-15 04:28:26 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-04-15 04:28:26 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-04-15 04:28:27 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-04-15 04:28:27 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-04-15 04:28:27 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-04-15 04:28:27 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-04-15 04:28:28 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-04-15 04:28:28 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-04-15 04:28:28 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-04-15 04:28:28 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-04-15 04:28:29 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-04-15 04:28:29 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-04-15 04:28:29 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-04-15 04:28:29 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-04-15 04:28:30 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-04-15 04:28:30 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-04-15 04:28:30 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-04-15 04:28:30 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-04-15 04:28:30 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-04-15 04:28:31 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-04-15 04:28:31 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-04-15 04:28:31 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-04-15 04:28:31 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-04-15 04:28:31 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-04-15 04:28:31 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-04-15 04:28:32 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-04-15 04:28:32 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-04-15 04:28:32 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-04-15 04:28:32 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-04-15 04:28:32 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-04-15 04:28:32 INFO::Fitting model to feature number 73, Dialister.invisus
2020-04-15 04:28:33 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-04-15 04:28:33 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-04-15 04:28:33 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-04-15 04:28:34 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-04-15 04:28:34 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-04-15 04:28:34 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-04-15 04:28:34 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-04-15 04:28:35 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-04-15 04:28:35 INFO::Fitting model to feature number 82, Escherichia.coli
2020-04-15 04:28:35 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-04-15 04:28:35 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-04-15 04:28:35 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-04-15 04:28:36 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-04-15 04:28:36 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-04-15 04:28:36 INFO::Counting total values for each feature
2020-04-15 04:28:36 INFO::Writing residuals to file output2/residuals.rds
2020-04-15 04:28:37 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2020-04-15 04:28:37 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): output2/significant_results.tsv
== testthat results  ===========================================================
[ OK: 9 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 3 ]
1. Failure: (unknown) (@test_Maaslin2.R#17) 
2. Failure: (unknown) (@test_Maaslin2.R#18) 
3. Failure: (unknown) (@test_Maaslin2.R#20) 

Error: testthat unit tests failed
Execution halted

Maaslin2.Rcheck/tests_x64/testthat.Rout.fail


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
2020-04-15 04:28:39 INFO::Writing function arguments to log file
2020-04-15 04:28:39 INFO::Verifying options selected are valid
2020-04-15 04:28:39 INFO::Determining format of input files
2020-04-15 04:28:39 INFO::Input format is data samples as rows and metadata samples as rows
2020-04-15 04:28:39 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-04-15 04:28:39 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2020-04-15 04:28:39 INFO::Running selected normalization method: TSS
2020-04-15 04:28:41 INFO::Filter data based on min abundance and min prevalence
2020-04-15 04:28:41 INFO::Total samples in data: 1595
2020-04-15 04:28:41 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-04-15 04:28:41 INFO::Total filtered features: 0
2020-04-15 04:28:41 INFO::Filtered feature names:
2020-04-15 04:28:41 INFO::Bypass z-score application to metadata
2020-04-15 04:28:41 INFO::Running selected transform method: AST
2020-04-15 04:28:41 INFO::Running selected analysis method: LM
2020-04-15 04:28:41 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-04-15 04:28:42 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-04-15 04:28:42 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-04-15 04:28:43 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-04-15 04:28:43 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-04-15 04:28:43 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-04-15 04:28:43 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-04-15 04:28:43 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-04-15 04:28:44 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-04-15 04:28:44 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-04-15 04:28:44 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-04-15 04:28:44 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-04-15 04:28:44 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-04-15 04:28:44 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-04-15 04:28:45 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-04-15 04:28:45 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-04-15 04:28:45 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-04-15 04:28:45 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-04-15 04:28:46 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-04-15 04:28:46 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-04-15 04:28:46 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-04-15 04:28:46 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-04-15 04:28:46 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-04-15 04:28:47 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-04-15 04:28:47 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-04-15 04:28:47 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-04-15 04:28:47 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-04-15 04:28:48 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-04-15 04:28:48 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-04-15 04:28:48 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-04-15 04:28:48 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-04-15 04:28:49 INFO::Fitting model to feature number 32, Prevotella.copri
2020-04-15 04:28:49 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-04-15 04:28:49 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-04-15 04:28:49 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-04-15 04:28:49 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-04-15 04:28:50 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-04-15 04:28:50 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-04-15 04:28:50 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-04-15 04:28:50 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-04-15 04:28:50 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-04-15 04:28:51 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-04-15 04:28:51 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-04-15 04:28:51 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-04-15 04:28:51 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-04-15 04:28:51 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-04-15 04:28:51 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-04-15 04:28:52 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-04-15 04:28:52 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-04-15 04:28:52 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-04-15 04:28:52 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-04-15 04:28:53 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-04-15 04:28:53 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-04-15 04:28:53 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-04-15 04:28:53 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-04-15 04:28:54 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-04-15 04:28:54 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-04-15 04:28:54 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-04-15 04:28:54 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-04-15 04:28:54 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-04-15 04:28:54 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-04-15 04:28:55 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-04-15 04:28:55 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-04-15 04:28:55 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-04-15 04:28:56 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-04-15 04:28:56 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-04-15 04:28:56 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-04-15 04:28:56 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-04-15 04:28:56 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-04-15 04:28:57 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-04-15 04:28:57 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-04-15 04:28:57 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-04-15 04:28:57 INFO::Fitting model to feature number 73, Dialister.invisus
2020-04-15 04:28:57 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-04-15 04:28:58 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-04-15 04:28:58 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-04-15 04:28:58 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-04-15 04:28:58 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-04-15 04:28:58 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-04-15 04:28:59 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-04-15 04:28:59 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-04-15 04:28:59 INFO::Fitting model to feature number 82, Escherichia.coli
2020-04-15 04:28:59 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-04-15 04:28:59 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-04-15 04:29:00 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-04-15 04:29:00 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-04-15 04:29:00 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-04-15 04:29:01 INFO::Counting total values for each feature
2020-04-15 04:29:01 INFO::Writing residuals to file output/residuals.rds
2020-04-15 04:29:01 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2020-04-15 04:29:01 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. Failure: (unknown) (@test_Maaslin2.R#17)  --------------------------------
`x` not equal to `expected`.
5/208 mismatches
x[133]: "dysbiosisUC"
y[133]: "diagnosis"

x[134]: "dysbiosisnonIBD"
y[134]: "dysbiosisUC"

x[135]: "diagnosis"
y[135]: "dysbiosisnonIBD"

x[185]: "antibiotics"
y[185]: "diagnosis"

x[187]: "diagnosis"
y[187]: "antibiotics"

-- 2. Failure: (unknown) (@test_Maaslin2.R#18)  --------------------------------
`x` not equal to `expected`.
10/208 mismatches
x[133]: "Clostridium.nexile"
y[133]: "Ruminococcus.callidus"

x[134]: "Lachnospiraceae.bacterium.3.1.46FAA"
y[134]: "Clostridium.nexile"

x[135]: "Ruminococcus.callidus"
y[135]: "Lachnospiraceae.bacterium.3.1.46FAA"

x[185]: "Veillonella.parvula"
y[185]: "Ruminococcus.gnavus"

x[186]: "Ruminococcus.gnavus"
y[186]: "Ruminococcus.obeum"

-- 3. Failure: (unknown) (@test_Maaslin2.R#20)  --------------------------------
`x` not equal to `expected`.
10/208 mismatches (average diff: 427)
[133]  273 -  323 ==  -50
[134]  992 -  273 ==  719
[135]  323 -  992 == -669
[185]  853 -  970 == -117
[186]  970 - 1346 == -376
[187] 1346 - 1514 == -168
[188] 1514 -  415 == 1099
[189]  415 -  853 == -438
[203]  730 -  415 ==  315
...

[1] "Creating output folder"
2020-04-15 04:29:01 INFO::Writing function arguments to log file
2020-04-15 04:29:01 INFO::Verifying options selected are valid
2020-04-15 04:29:01 INFO::Determining format of input files
2020-04-15 04:29:01 INFO::Input format is data samples as rows and metadata samples as rows
2020-04-15 04:29:01 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2020-04-15 04:29:01 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2020-04-15 04:29:01 INFO::Running selected normalization method: NONE
2020-04-15 04:29:01 INFO::Filter data based on min abundance and min prevalence
2020-04-15 04:29:01 INFO::Total samples in data: 1595
2020-04-15 04:29:01 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2020-04-15 04:29:01 INFO::Total filtered features: 0
2020-04-15 04:29:01 INFO::Filtered feature names:
2020-04-15 04:29:01 INFO::Bypass z-score application to metadata
2020-04-15 04:29:01 INFO::Running selected transform method: AST
2020-04-15 04:29:01 INFO::Running selected analysis method: LM
2020-04-15 04:29:01 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2020-04-15 04:29:01 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2020-04-15 04:29:01 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2020-04-15 04:29:01 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2020-04-15 04:29:01 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2020-04-15 04:29:02 INFO::Fitting model to feature number 6, Bacteroides.caccae
2020-04-15 04:29:02 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2020-04-15 04:29:02 INFO::Fitting model to feature number 8, Bacteroides.dorei
2020-04-15 04:29:02 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2020-04-15 04:29:03 INFO::Fitting model to feature number 10, Bacteroides.faecis
2020-04-15 04:29:03 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2020-04-15 04:29:03 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2020-04-15 04:29:03 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2020-04-15 04:29:03 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2020-04-15 04:29:04 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2020-04-15 04:29:04 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2020-04-15 04:29:04 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2020-04-15 04:29:04 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2020-04-15 04:29:05 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2020-04-15 04:29:05 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2020-04-15 04:29:05 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2020-04-15 04:29:05 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2020-04-15 04:29:06 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2020-04-15 04:29:06 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2020-04-15 04:29:06 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2020-04-15 04:29:06 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2020-04-15 04:29:06 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2020-04-15 04:29:07 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2020-04-15 04:29:07 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2020-04-15 04:29:07 INFO::Fitting model to feature number 30, Paraprevotella.clara
2020-04-15 04:29:07 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2020-04-15 04:29:07 INFO::Fitting model to feature number 32, Prevotella.copri
2020-04-15 04:29:08 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2020-04-15 04:29:08 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2020-04-15 04:29:08 INFO::Fitting model to feature number 35, Alistipes.putredinis
2020-04-15 04:29:08 INFO::Fitting model to feature number 36, Alistipes.shahii
2020-04-15 04:29:09 INFO::Fitting model to feature number 37, Alistipes.unclassified
2020-04-15 04:29:09 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2020-04-15 04:29:09 INFO::Fitting model to feature number 39, Clostridium.bolteae
2020-04-15 04:29:09 INFO::Fitting model to feature number 40, Clostridium.citroniae
2020-04-15 04:29:09 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2020-04-15 04:29:10 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2020-04-15 04:29:10 INFO::Fitting model to feature number 43, Clostridium.leptum
2020-04-15 04:29:10 INFO::Fitting model to feature number 44, Clostridium.nexile
2020-04-15 04:29:10 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2020-04-15 04:29:10 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2020-04-15 04:29:11 INFO::Fitting model to feature number 47, Eubacterium.eligens
2020-04-15 04:29:11 INFO::Fitting model to feature number 48, Eubacterium.hallii
2020-04-15 04:29:11 INFO::Fitting model to feature number 49, Eubacterium.rectale
2020-04-15 04:29:11 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2020-04-15 04:29:11 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2020-04-15 04:29:12 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2020-04-15 04:29:12 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2020-04-15 04:29:12 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2020-04-15 04:29:12 INFO::Fitting model to feature number 55, Ruminococcus.torques
2020-04-15 04:29:12 INFO::Fitting model to feature number 56, Coprococcus.comes
2020-04-15 04:29:13 INFO::Fitting model to feature number 57, Dorea.longicatena
2020-04-15 04:29:13 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2020-04-15 04:29:13 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2020-04-15 04:29:13 INFO::Fitting model to feature number 60, Roseburia.hominis
2020-04-15 04:29:13 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2020-04-15 04:29:14 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2020-04-15 04:29:14 INFO::Fitting model to feature number 63, Roseburia.unclassified
2020-04-15 04:29:14 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2020-04-15 04:29:14 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2020-04-15 04:29:15 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2020-04-15 04:29:15 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2020-04-15 04:29:15 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2020-04-15 04:29:15 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2020-04-15 04:29:16 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2020-04-15 04:29:16 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2020-04-15 04:29:16 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2020-04-15 04:29:16 INFO::Fitting model to feature number 73, Dialister.invisus
2020-04-15 04:29:16 INFO::Fitting model to feature number 74, Veillonella.atypica
2020-04-15 04:29:17 INFO::Fitting model to feature number 75, Veillonella.dispar
2020-04-15 04:29:17 INFO::Fitting model to feature number 76, Veillonella.parvula
2020-04-15 04:29:17 INFO::Fitting model to feature number 77, Veillonella.unclassified
2020-04-15 04:29:17 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2020-04-15 04:29:18 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2020-04-15 04:29:18 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2020-04-15 04:29:18 INFO::Fitting model to feature number 81, Bilophila.unclassified
2020-04-15 04:29:18 INFO::Fitting model to feature number 82, Escherichia.coli
2020-04-15 04:29:18 INFO::Fitting model to feature number 83, Escherichia.unclassified
2020-04-15 04:29:19 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2020-04-15 04:29:19 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2020-04-15 04:29:20 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2020-04-15 04:29:20 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2020-04-15 04:29:20 INFO::Counting total values for each feature
2020-04-15 04:29:20 INFO::Writing residuals to file output2/residuals.rds
2020-04-15 04:29:20 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2020-04-15 04:29:20 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
== testthat results  ===========================================================
[ OK: 9 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 3 ]
1. Failure: (unknown) (@test_Maaslin2.R#17) 
2. Failure: (unknown) (@test_Maaslin2.R#18) 
3. Failure: (unknown) (@test_Maaslin2.R#20) 

Error: testthat unit tests failed
Execution halted

Example timings

Maaslin2.Rcheck/examples_i386/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin295.94 0.6998.75

Maaslin2.Rcheck/examples_x64/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin279.95 0.6481.82