##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Maaslin2_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Maaslin2: no visible global function definition for ‘type.convert’
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  type.convert xnames
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Maaslin2 108.733  0.731  109.47
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘maaslin2.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* 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 1.5.3
Current Matrix version is 1.5.4
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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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"
2023-04-12 07:11:56.258227 INFO::Writing function arguments to log file
2023-04-12 07:11:56.285124 INFO::Verifying options selected are valid
2023-04-12 07:11:56.323507 INFO::Determining format of input files
2023-04-12 07:11:56.325347 INFO::Input format is data samples as rows and metadata samples as rows
2023-04-12 07:11:56.330404 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-04-12 07:11:56.331865 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-04-12 07:11:56.334068 INFO::Filter data based on min abundance and min prevalence
2023-04-12 07:11:56.335025 INFO::Total samples in data: 1595
2023-04-12 07:11:56.33592 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-04-12 07:11:56.340163 INFO::Total filtered features: 0
2023-04-12 07:11:56.351082 INFO::Filtered feature names from abundance and prevalence filtering:
2023-04-12 07:11:56.358386 INFO::Total filtered features with variance filtering: 0
2023-04-12 07:11:56.359706 INFO::Filtered feature names from variance filtering:
2023-04-12 07:11:56.360606 INFO::Running selected normalization method: TSS
2023-04-12 07:11:57.708557 INFO::Bypass z-score application to metadata
2023-04-12 07:11:57.710136 INFO::Running selected transform method: AST
2023-04-12 07:11:57.739912 INFO::Running selected analysis method: LM
2023-04-12 07:11:58.560357 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-04-12 07:11:58.998947 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-04-12 07:11:59.183836 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-04-12 07:11:59.357233 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-04-12 07:11:59.530713 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-04-12 07:11:59.709169 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-04-12 07:11:59.877959 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-04-12 07:12:00.052539 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-04-12 07:12:00.263528 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-04-12 07:12:00.444352 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-04-12 07:12:00.619154 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-04-12 07:12:00.796749 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-04-12 07:12:00.98695 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-04-12 07:12:01.175553 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-04-12 07:12:01.391513 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-04-12 07:12:01.585695 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-04-12 07:12:01.74774 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-04-12 07:12:01.922746 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-04-12 07:12:02.109088 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-04-12 07:12:02.269411 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-04-12 07:12:02.438566 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-04-12 07:12:02.629374 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-04-12 07:12:02.79073 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-04-12 07:12:02.952479 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-04-12 07:12:03.121858 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-04-12 07:12:03.287682 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-04-12 07:12:03.444429 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-04-12 07:12:03.627155 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-04-12 07:12:03.787514 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-04-12 07:12:03.950342 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-04-12 07:12:04.117057 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-04-12 07:12:04.284586 INFO::Fitting model to feature number 32, Prevotella.copri
2023-04-12 07:12:04.485062 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-04-12 07:12:04.668892 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-04-12 07:12:04.830107 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-04-12 07:12:05.007556 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-04-12 07:12:05.179993 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-04-12 07:12:05.356178 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-04-12 07:12:05.533823 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-04-12 07:12:05.751435 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-04-12 07:12:05.924994 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-04-12 07:12:06.095354 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-04-12 07:12:06.273104 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-04-12 07:12:06.444675 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-04-12 07:12:06.604484 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-04-12 07:12:06.768914 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-04-12 07:12:06.930608 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-04-12 07:12:07.108409 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-04-12 07:12:07.338625 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-04-12 07:12:07.499419 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-04-12 07:12:07.668396 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-04-12 07:12:07.896425 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-04-12 07:12:08.068939 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-04-12 07:12:08.263097 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-04-12 07:12:08.453002 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-04-12 07:12:08.639733 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-04-12 07:12:08.837445 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-04-12 07:12:09.015055 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-04-12 07:12:09.229368 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-04-12 07:12:09.391053 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-04-12 07:12:09.554464 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-04-12 07:12:09.720788 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-04-12 07:12:09.901057 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-04-12 07:12:10.476009 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-04-12 07:12:10.72858 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-04-12 07:12:10.905649 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-04-12 07:12:11.067306 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-04-12 07:12:11.245277 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-04-12 07:12:11.417936 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-04-12 07:12:11.603745 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-04-12 07:12:11.806558 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-04-12 07:12:11.981496 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-04-12 07:12:12.174253 INFO::Fitting model to feature number 73, Dialister.invisus
2023-04-12 07:12:12.347749 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-04-12 07:12:12.518362 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-04-12 07:12:12.685671 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-04-12 07:12:12.856571 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-04-12 07:12:13.019954 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-04-12 07:12:13.194955 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-04-12 07:12:13.367841 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-04-12 07:12:13.53057 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-04-12 07:12:13.71598 INFO::Fitting model to feature number 82, Escherichia.coli
2023-04-12 07:12:13.885758 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-04-12 07:12:14.034773 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-04-12 07:12:14.201993 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-04-12 07:12:14.479726 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-04-12 07:12:14.70731 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-04-12 07:12:14.926929 INFO::Counting total values for each feature
2023-04-12 07:12:14.960625 INFO::Writing residuals to file output/residuals.rds
2023-04-12 07:12:15.017036 INFO::Writing fitted values to file output/fitted.rds
2023-04-12 07:12:15.048612 INFO::Writing extracted random effects to file output/ranef.rds
2023-04-12 07:12:15.054472 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-04-12 07:12:15.062022 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"
2023-04-12 07:12:15.073193 INFO::Writing function arguments to log file
2023-04-12 07:12:15.078749 INFO::Verifying options selected are valid
2023-04-12 07:12:15.079764 INFO::Determining format of input files
2023-04-12 07:12:15.080852 INFO::Input format is data samples as rows and metadata samples as rows
2023-04-12 07:12:15.097333 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-04-12 07:12:15.098722 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-04-12 07:12:15.105047 INFO::Filter data based on min abundance and min prevalence
2023-04-12 07:12:15.106168 INFO::Total samples in data: 1595
2023-04-12 07:12:15.107103 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-04-12 07:12:15.112135 INFO::Total filtered features: 0
2023-04-12 07:12:15.113258 INFO::Filtered feature names from abundance and prevalence filtering:
2023-04-12 07:12:15.121584 INFO::Total filtered features with variance filtering: 0
2023-04-12 07:12:15.122951 INFO::Filtered feature names from variance filtering:
2023-04-12 07:12:15.123928 INFO::Running selected normalization method: NONE
2023-04-12 07:12:15.124799 INFO::Bypass z-score application to metadata
2023-04-12 07:12:15.125651 INFO::Running selected transform method: AST
2023-04-12 07:12:15.141664 INFO::Running selected analysis method: LM
2023-04-12 07:12:15.143666 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-04-12 07:12:15.30105 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-04-12 07:12:15.462832 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-04-12 07:12:15.645407 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-04-12 07:12:15.804588 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-04-12 07:12:15.95244 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-04-12 07:12:16.109721 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-04-12 07:12:16.271997 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-04-12 07:12:16.431571 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-04-12 07:12:16.703877 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-04-12 07:12:16.899735 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-04-12 07:12:17.067681 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-04-12 07:12:17.22511 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-04-12 07:12:17.379027 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-04-12 07:12:17.541323 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-04-12 07:12:17.713498 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-04-12 07:12:17.858907 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-04-12 07:12:18.022404 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-04-12 07:12:18.187785 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-04-12 07:12:18.332058 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-04-12 07:12:18.495637 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-04-12 07:12:18.653655 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-04-12 07:12:18.820432 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-04-12 07:12:18.974293 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-04-12 07:12:19.145252 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-04-12 07:12:19.317902 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-04-12 07:12:19.482983 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-04-12 07:12:19.690318 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-04-12 07:12:19.865515 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-04-12 07:12:20.06207 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-04-12 07:12:20.231089 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-04-12 07:12:20.394901 INFO::Fitting model to feature number 32, Prevotella.copri
2023-04-12 07:12:20.565756 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-04-12 07:12:20.726122 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-04-12 07:12:20.887087 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-04-12 07:12:21.056102 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-04-12 07:12:21.2239 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-04-12 07:12:21.381569 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-04-12 07:12:21.550402 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-04-12 07:12:21.693978 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-04-12 07:12:21.841393 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-04-12 07:12:22.014921 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-04-12 07:12:22.171463 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-04-12 07:12:22.326499 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-04-12 07:12:22.491967 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-04-12 07:12:22.67557 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-04-12 07:12:22.884851 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-04-12 07:12:23.029247 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-04-12 07:12:23.178177 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-04-12 07:12:23.37201 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-04-12 07:12:23.521228 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-04-12 07:12:23.685929 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-04-12 07:12:23.838443 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-04-12 07:12:23.993273 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-04-12 07:12:24.210844 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-04-12 07:12:24.386711 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-04-12 07:12:24.552408 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-04-12 07:12:24.762098 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-04-12 07:12:24.969343 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-04-12 07:12:25.11785 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-04-12 07:12:25.2654 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-04-12 07:12:25.421003 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-04-12 07:12:25.57768 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-04-12 07:12:25.729377 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-04-12 07:12:25.945525 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-04-12 07:12:26.107726 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-04-12 07:12:26.27545 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-04-12 07:12:26.427135 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-04-12 07:12:26.584625 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-04-12 07:12:26.744038 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-04-12 07:12:26.92704 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-04-12 07:12:27.089329 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-04-12 07:12:27.248185 INFO::Fitting model to feature number 73, Dialister.invisus
2023-04-12 07:12:27.404206 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-04-12 07:12:27.55935 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-04-12 07:12:27.714023 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-04-12 07:12:27.861093 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-04-12 07:12:28.015772 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-04-12 07:12:28.160651 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-04-12 07:12:28.310118 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-04-12 07:12:28.455014 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-04-12 07:12:28.61238 INFO::Fitting model to feature number 82, Escherichia.coli
2023-04-12 07:12:28.754665 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-04-12 07:12:28.893801 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-04-12 07:12:29.045798 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-04-12 07:12:29.190168 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-04-12 07:12:29.353307 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-04-12 07:12:29.559818 INFO::Counting total values for each feature
2023-04-12 07:12:29.58668 INFO::Writing residuals to file output2/residuals.rds
2023-04-12 07:12:29.661236 INFO::Writing fitted values to file output2/fitted.rds
2023-04-12 07:12:29.733025 INFO::Writing extracted random effects to file output2/ranef.rds
2023-04-12 07:12:29.739076 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-04-12 07:12:29.745148 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 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 34.637   0.564  35.189