##############################################################################
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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/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) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 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 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 90.424  0.856  91.221
* 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/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 1.9.1
Current TMB version is 1.9.2
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 Under development (unstable) (2023-01-10 r83596) -- "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"
2023-03-15 21:19:53.323853 INFO::Writing function arguments to log file
2023-03-15 21:19:53.348705 INFO::Verifying options selected are valid
2023-03-15 21:19:53.384487 INFO::Determining format of input files
2023-03-15 21:19:53.3859 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 21:19:53.390383 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-03-15 21:19:53.391667 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-03-15 21:19:53.393738 INFO::Filter data based on min abundance and min prevalence
2023-03-15 21:19:53.394635 INFO::Total samples in data: 1595
2023-03-15 21:19:53.395453 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-03-15 21:19:53.399107 INFO::Total filtered features: 0
2023-03-15 21:19:53.407504 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 21:19:53.413855 INFO::Total filtered features with variance filtering: 0
2023-03-15 21:19:53.414857 INFO::Filtered feature names from variance filtering:
2023-03-15 21:19:53.415697 INFO::Running selected normalization method: TSS
2023-03-15 21:19:54.641232 INFO::Bypass z-score application to metadata
2023-03-15 21:19:54.642994 INFO::Running selected transform method: AST
2023-03-15 21:19:54.675853 INFO::Running selected analysis method: LM
2023-03-15 21:19:55.348946 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-03-15 21:19:55.78149 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-03-15 21:19:55.962085 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-03-15 21:19:56.123442 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-03-15 21:19:56.298078 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-03-15 21:19:56.48096 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-03-15 21:19:56.651134 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-03-15 21:19:56.827532 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-03-15 21:19:57.028545 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-03-15 21:19:57.215497 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-03-15 21:19:57.379537 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-03-15 21:19:57.543773 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-03-15 21:19:57.712217 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-03-15 21:19:57.885559 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-03-15 21:19:58.049443 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-03-15 21:19:58.226401 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-03-15 21:19:58.452892 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-03-15 21:19:58.635983 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-03-15 21:19:58.875567 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-03-15 21:19:59.040005 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-03-15 21:19:59.186286 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-03-15 21:19:59.345374 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-03-15 21:19:59.533998 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-03-15 21:19:59.716678 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-03-15 21:19:59.92091 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-03-15 21:20:00.100536 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-03-15 21:20:00.265437 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-03-15 21:20:00.443508 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-03-15 21:20:00.609548 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-03-15 21:20:00.817028 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-03-15 21:20:01.570025 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-03-15 21:20:01.723068 INFO::Fitting model to feature number 32, Prevotella.copri
2023-03-15 21:20:01.879203 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-03-15 21:20:02.051861 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-03-15 21:20:02.205921 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-03-15 21:20:02.365164 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-03-15 21:20:02.528231 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-03-15 21:20:02.699227 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-03-15 21:20:02.851267 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-03-15 21:20:03.002339 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-03-15 21:20:03.178177 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-03-15 21:20:03.331227 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-03-15 21:20:03.493389 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-03-15 21:20:03.64893 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-03-15 21:20:03.810473 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-03-15 21:20:03.982764 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-03-15 21:20:04.170137 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-03-15 21:20:04.334967 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-03-15 21:20:04.490676 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-03-15 21:20:04.64519 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-03-15 21:20:04.788971 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-03-15 21:20:04.9429 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-03-15 21:20:05.093716 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-03-15 21:20:05.256892 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-03-15 21:20:05.416832 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-03-15 21:20:05.579114 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-03-15 21:20:05.750635 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-03-15 21:20:05.908753 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-03-15 21:20:06.058805 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-03-15 21:20:06.214208 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-03-15 21:20:06.362566 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-03-15 21:20:06.522525 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-03-15 21:20:06.67957 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-03-15 21:20:06.831857 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-03-15 21:20:06.982394 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-03-15 21:20:07.125963 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-03-15 21:20:07.287922 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-03-15 21:20:07.437231 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-03-15 21:20:07.60445 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-03-15 21:20:07.771415 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-03-15 21:20:07.967248 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-03-15 21:20:08.13384 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-03-15 21:20:08.295533 INFO::Fitting model to feature number 73, Dialister.invisus
2023-03-15 21:20:08.457719 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-03-15 21:20:08.613446 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-03-15 21:20:08.767024 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-03-15 21:20:08.924072 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-03-15 21:20:09.074328 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-03-15 21:20:09.235065 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-03-15 21:20:09.398046 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-03-15 21:20:09.552382 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-03-15 21:20:09.710695 INFO::Fitting model to feature number 82, Escherichia.coli
2023-03-15 21:20:09.877822 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-03-15 21:20:10.040446 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-03-15 21:20:10.200701 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-03-15 21:20:10.356018 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-03-15 21:20:10.501331 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-03-15 21:20:10.7012 INFO::Counting total values for each feature
2023-03-15 21:20:10.73367 INFO::Writing residuals to file output/residuals.rds
2023-03-15 21:20:10.790602 INFO::Writing fitted values to file output/fitted.rds
2023-03-15 21:20:10.822176 INFO::Writing extracted random effects to file output/ranef.rds
2023-03-15 21:20:10.82808 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-03-15 21:20:10.835336 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"
2023-03-15 21:20:10.8468 INFO::Writing function arguments to log file
2023-03-15 21:20:10.852744 INFO::Verifying options selected are valid
2023-03-15 21:20:10.853727 INFO::Determining format of input files
2023-03-15 21:20:10.854805 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-15 21:20:10.859374 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-03-15 21:20:10.860451 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-03-15 21:20:10.866022 INFO::Filter data based on min abundance and min prevalence
2023-03-15 21:20:10.866934 INFO::Total samples in data: 1595
2023-03-15 21:20:10.867767 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-03-15 21:20:10.871976 INFO::Total filtered features: 0
2023-03-15 21:20:10.872949 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-15 21:20:10.880193 INFO::Total filtered features with variance filtering: 0
2023-03-15 21:20:10.881254 INFO::Filtered feature names from variance filtering:
2023-03-15 21:20:10.882102 INFO::Running selected normalization method: NONE
2023-03-15 21:20:10.882907 INFO::Bypass z-score application to metadata
2023-03-15 21:20:10.8837 INFO::Running selected transform method: AST
2023-03-15 21:20:10.90513 INFO::Running selected analysis method: LM
2023-03-15 21:20:10.907076 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-03-15 21:20:11.048444 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-03-15 21:20:11.202699 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-03-15 21:20:11.341475 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-03-15 21:20:11.492912 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-03-15 21:20:11.632299 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-03-15 21:20:11.787812 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-03-15 21:20:11.949186 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-03-15 21:20:12.094973 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-03-15 21:20:12.259512 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-03-15 21:20:12.720684 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-03-15 21:20:12.897875 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-03-15 21:20:13.055984 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-03-15 21:20:13.21536 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-03-15 21:20:13.38247 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-03-15 21:20:13.533844 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-03-15 21:20:13.684825 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-03-15 21:20:13.854134 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-03-15 21:20:14.017067 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-03-15 21:20:14.165257 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-03-15 21:20:14.314394 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-03-15 21:20:14.477243 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-03-15 21:20:14.625846 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-03-15 21:20:14.77083 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-03-15 21:20:14.934571 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-03-15 21:20:15.08115 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-03-15 21:20:15.226327 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-03-15 21:20:15.378707 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-03-15 21:20:15.527708 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-03-15 21:20:15.672287 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-03-15 21:20:15.82003 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-03-15 21:20:15.982951 INFO::Fitting model to feature number 32, Prevotella.copri
2023-03-15 21:20:16.138446 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-03-15 21:20:16.295257 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-03-15 21:20:16.452504 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-03-15 21:20:16.602807 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-03-15 21:20:16.755696 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-03-15 21:20:16.914189 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-03-15 21:20:17.065981 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-03-15 21:20:17.207881 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-03-15 21:20:17.36135 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-03-15 21:20:17.506053 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-03-15 21:20:17.652507 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-03-15 21:20:17.827511 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-03-15 21:20:17.975797 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-03-15 21:20:18.124379 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-03-15 21:20:18.282352 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-03-15 21:20:18.44965 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-03-15 21:20:18.604814 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-03-15 21:20:18.760655 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-03-15 21:20:18.915604 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-03-15 21:20:19.062168 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-03-15 21:20:19.197856 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-03-15 21:20:19.341605 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-03-15 21:20:19.487502 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-03-15 21:20:19.659428 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-03-15 21:20:19.844818 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-03-15 21:20:20.001027 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-03-15 21:20:20.149055 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-03-15 21:20:20.306831 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-03-15 21:20:20.445141 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-03-15 21:20:20.589567 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-03-15 21:20:20.738835 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-03-15 21:20:20.886566 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-03-15 21:20:21.035159 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-03-15 21:20:21.195773 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-03-15 21:20:21.348555 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-03-15 21:20:21.527718 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-03-15 21:20:21.680753 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-03-15 21:20:21.827605 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-03-15 21:20:21.988903 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-03-15 21:20:22.12868 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-03-15 21:20:22.279715 INFO::Fitting model to feature number 73, Dialister.invisus
2023-03-15 21:20:22.421224 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-03-15 21:20:22.577233 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-03-15 21:20:22.722622 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-03-15 21:20:22.88438 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-03-15 21:20:23.02746 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-03-15 21:20:23.185897 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-03-15 21:20:23.340192 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-03-15 21:20:23.512602 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-03-15 21:20:23.670842 INFO::Fitting model to feature number 82, Escherichia.coli
2023-03-15 21:20:23.834321 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-03-15 21:20:23.988166 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-03-15 21:20:24.134505 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-03-15 21:20:24.31225 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-03-15 21:20:24.461872 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-03-15 21:20:24.649776 INFO::Counting total values for each feature
2023-03-15 21:20:24.685098 INFO::Writing residuals to file output2/residuals.rds
2023-03-15 21:20:24.759825 INFO::Writing fitted values to file output2/fitted.rds
2023-03-15 21:20:24.831911 INFO::Writing extracted random effects to file output2/ranef.rds
2023-03-15 21:20:24.837775 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-03-15 21:20:24.843218 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 9 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 31.834   0.911  32.736