##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Maaslin2_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Maaslin2.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘lme4’
Namespace in Imports field not imported from: ‘MuMIn’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Maaslin2 104.778    1.4 106.712
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.7.21
Current TMB version is 1.7.22
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** 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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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

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

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

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
2021-10-14 20:37:42 INFO::Writing function arguments to log file
2021-10-14 20:37:42 INFO::Verifying options selected are valid
2021-10-14 20:37:42 INFO::Determining format of input files
2021-10-14 20:37:42 INFO::Input format is data samples as rows and metadata samples as rows
2021-10-14 20:37:42 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-10-14 20:37:42 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2021-10-14 20:37:42 INFO::Filter data based on min abundance and min prevalence
2021-10-14 20:37:42 INFO::Total samples in data: 1595
2021-10-14 20:37:42 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-10-14 20:37:42 INFO::Total filtered features: 0
2021-10-14 20:37:42 INFO::Filtered feature names from abundance and prevalence filtering:
2021-10-14 20:37:42 INFO::Total filtered features with variance filtering: 0
2021-10-14 20:37:42 INFO::Filtered feature names from variance filtering:
2021-10-14 20:37:42 INFO::Running selected normalization method: TSS
2021-10-14 20:37:44 INFO::Bypass z-score application to metadata
2021-10-14 20:37:44 INFO::Running selected transform method: AST
2021-10-14 20:37:44 INFO::Running selected analysis method: LM
2021-10-14 20:37:45 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-10-14 20:37:46 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-10-14 20:37:46 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-10-14 20:37:46 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-10-14 20:37:46 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-10-14 20:37:47 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-10-14 20:37:47 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-10-14 20:37:47 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-10-14 20:37:47 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-10-14 20:37:48 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-10-14 20:37:48 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-10-14 20:37:48 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-10-14 20:37:48 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-10-14 20:37:49 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-10-14 20:37:49 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-10-14 20:37:49 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-10-14 20:37:49 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-10-14 20:37:49 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-10-14 20:37:50 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-10-14 20:37:50 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-10-14 20:37:50 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-10-14 20:37:50 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-10-14 20:37:50 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-10-14 20:37:51 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-10-14 20:37:51 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-10-14 20:37:51 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-10-14 20:37:51 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-10-14 20:37:52 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-10-14 20:37:52 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-10-14 20:37:52 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-10-14 20:37:52 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-10-14 20:37:53 INFO::Fitting model to feature number 32, Prevotella.copri
2021-10-14 20:37:53 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-10-14 20:37:53 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-10-14 20:37:53 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-10-14 20:37:53 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-10-14 20:37:54 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-10-14 20:37:54 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-10-14 20:37:54 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-10-14 20:37:54 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-10-14 20:37:54 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-10-14 20:37:55 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-10-14 20:37:55 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-10-14 20:37:55 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-10-14 20:37:55 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-10-14 20:37:55 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-10-14 20:37:56 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-10-14 20:37:56 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-10-14 20:37:56 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-10-14 20:37:56 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-10-14 20:37:56 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-10-14 20:37:57 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-10-14 20:37:57 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-10-14 20:37:57 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-10-14 20:37:57 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-10-14 20:37:57 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-10-14 20:37:58 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-10-14 20:37:58 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-10-14 20:37:58 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-10-14 20:37:58 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-10-14 20:37:58 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-10-14 20:37:59 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-10-14 20:37:59 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-10-14 20:37:59 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-10-14 20:37:59 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-10-14 20:37:59 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-10-14 20:38:00 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-10-14 20:38:00 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-10-14 20:38:00 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-10-14 20:38:00 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-10-14 20:38:00 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-10-14 20:38:01 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-10-14 20:38:01 INFO::Fitting model to feature number 73, Dialister.invisus
2021-10-14 20:38:01 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-10-14 20:38:01 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-10-14 20:38:02 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-10-14 20:38:02 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-10-14 20:38:02 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-10-14 20:38:02 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-10-14 20:38:02 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-10-14 20:38:03 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-10-14 20:38:03 INFO::Fitting model to feature number 82, Escherichia.coli
2021-10-14 20:38:03 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-10-14 20:38:03 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-10-14 20:38:04 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-10-14 20:38:04 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-10-14 20:38:04 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-10-14 20:38:04 INFO::Counting total values for each feature
2021-10-14 20:38:04 INFO::Writing residuals to file output/residuals.rds
2021-10-14 20:38:04 INFO::Writing fitted values to file output/fitted.rds
2021-10-14 20:38:04 INFO::Writing extracted random effects to file output/ranef.rds
2021-10-14 20:38:04 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2021-10-14 20:38:04 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
2021-10-14 20:38:04 INFO::Writing function arguments to log file
2021-10-14 20:38:04 INFO::Verifying options selected are valid
2021-10-14 20:38:04 INFO::Determining format of input files
2021-10-14 20:38:04 INFO::Input format is data samples as rows and metadata samples as rows
2021-10-14 20:38:04 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2021-10-14 20:38:04 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2021-10-14 20:38:04 INFO::Filter data based on min abundance and min prevalence
2021-10-14 20:38:04 INFO::Total samples in data: 1595
2021-10-14 20:38:04 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2021-10-14 20:38:04 INFO::Total filtered features: 0
2021-10-14 20:38:04 INFO::Filtered feature names from abundance and prevalence filtering:
2021-10-14 20:38:04 INFO::Total filtered features with variance filtering: 0
2021-10-14 20:38:04 INFO::Filtered feature names from variance filtering:
2021-10-14 20:38:04 INFO::Running selected normalization method: NONE
2021-10-14 20:38:04 INFO::Bypass z-score application to metadata
2021-10-14 20:38:04 INFO::Running selected transform method: AST
2021-10-14 20:38:04 INFO::Running selected analysis method: LM
2021-10-14 20:38:04 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2021-10-14 20:38:05 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2021-10-14 20:38:05 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2021-10-14 20:38:05 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2021-10-14 20:38:05 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2021-10-14 20:38:06 INFO::Fitting model to feature number 6, Bacteroides.caccae
2021-10-14 20:38:06 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2021-10-14 20:38:06 INFO::Fitting model to feature number 8, Bacteroides.dorei
2021-10-14 20:38:06 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2021-10-14 20:38:07 INFO::Fitting model to feature number 10, Bacteroides.faecis
2021-10-14 20:38:07 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2021-10-14 20:38:07 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2021-10-14 20:38:07 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2021-10-14 20:38:07 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2021-10-14 20:38:08 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2021-10-14 20:38:08 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2021-10-14 20:38:08 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2021-10-14 20:38:08 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2021-10-14 20:38:09 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2021-10-14 20:38:09 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2021-10-14 20:38:09 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2021-10-14 20:38:09 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2021-10-14 20:38:10 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2021-10-14 20:38:10 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2021-10-14 20:38:10 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2021-10-14 20:38:10 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2021-10-14 20:38:11 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2021-10-14 20:38:11 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2021-10-14 20:38:11 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2021-10-14 20:38:11 INFO::Fitting model to feature number 30, Paraprevotella.clara
2021-10-14 20:38:12 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2021-10-14 20:38:12 INFO::Fitting model to feature number 32, Prevotella.copri
2021-10-14 20:38:12 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2021-10-14 20:38:12 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2021-10-14 20:38:12 INFO::Fitting model to feature number 35, Alistipes.putredinis
2021-10-14 20:38:13 INFO::Fitting model to feature number 36, Alistipes.shahii
2021-10-14 20:38:13 INFO::Fitting model to feature number 37, Alistipes.unclassified
2021-10-14 20:38:13 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2021-10-14 20:38:13 INFO::Fitting model to feature number 39, Clostridium.bolteae
2021-10-14 20:38:13 INFO::Fitting model to feature number 40, Clostridium.citroniae
2021-10-14 20:38:14 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2021-10-14 20:38:14 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2021-10-14 20:38:14 INFO::Fitting model to feature number 43, Clostridium.leptum
2021-10-14 20:38:15 INFO::Fitting model to feature number 44, Clostridium.nexile
2021-10-14 20:38:15 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2021-10-14 20:38:15 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2021-10-14 20:38:15 INFO::Fitting model to feature number 47, Eubacterium.eligens
2021-10-14 20:38:15 INFO::Fitting model to feature number 48, Eubacterium.hallii
2021-10-14 20:38:16 INFO::Fitting model to feature number 49, Eubacterium.rectale
2021-10-14 20:38:16 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2021-10-14 20:38:16 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2021-10-14 20:38:16 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2021-10-14 20:38:16 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2021-10-14 20:38:17 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2021-10-14 20:38:17 INFO::Fitting model to feature number 55, Ruminococcus.torques
2021-10-14 20:38:17 INFO::Fitting model to feature number 56, Coprococcus.comes
2021-10-14 20:38:18 INFO::Fitting model to feature number 57, Dorea.longicatena
2021-10-14 20:38:18 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2021-10-14 20:38:18 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2021-10-14 20:38:18 INFO::Fitting model to feature number 60, Roseburia.hominis
2021-10-14 20:38:18 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2021-10-14 20:38:18 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2021-10-14 20:38:19 INFO::Fitting model to feature number 63, Roseburia.unclassified
2021-10-14 20:38:19 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2021-10-14 20:38:19 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2021-10-14 20:38:19 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2021-10-14 20:38:20 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2021-10-14 20:38:20 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2021-10-14 20:38:20 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2021-10-14 20:38:20 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2021-10-14 20:38:21 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2021-10-14 20:38:21 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2021-10-14 20:38:21 INFO::Fitting model to feature number 73, Dialister.invisus
2021-10-14 20:38:21 INFO::Fitting model to feature number 74, Veillonella.atypica
2021-10-14 20:38:22 INFO::Fitting model to feature number 75, Veillonella.dispar
2021-10-14 20:38:22 INFO::Fitting model to feature number 76, Veillonella.parvula
2021-10-14 20:38:22 INFO::Fitting model to feature number 77, Veillonella.unclassified
2021-10-14 20:38:22 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2021-10-14 20:38:22 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2021-10-14 20:38:22 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2021-10-14 20:38:23 INFO::Fitting model to feature number 81, Bilophila.unclassified
2021-10-14 20:38:23 INFO::Fitting model to feature number 82, Escherichia.coli
2021-10-14 20:38:23 INFO::Fitting model to feature number 83, Escherichia.unclassified
2021-10-14 20:38:23 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2021-10-14 20:38:24 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2021-10-14 20:38:24 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2021-10-14 20:38:24 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2021-10-14 20:38:24 INFO::Counting total values for each feature
2021-10-14 20:38:24 INFO::Writing residuals to file output2/residuals.rds
2021-10-14 20:38:25 INFO::Writing fitted values to file output2/fitted.rds
2021-10-14 20:38:25 INFO::Writing extracted random effects to file output2/ranef.rds
2021-10-14 20:38:25 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2021-10-14 20:38:25 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 ]
> 
> 
> proc.time()
   user  system elapsed 
 43.399   0.653  44.082