##############################################################################
##############################################################################
###
### 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.14.1’
* 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_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 88.398  0.859    89.2
* 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.

##############################################################################
##############################################################################
###
### 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 1.6.0
Current Matrix version is 1.6.1.1
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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2023-10-15 22:27:42.473552 INFO::Writing function arguments to log file
2023-10-15 22:27:42.498379 INFO::Verifying options selected are valid
2023-10-15 22:27:42.533566 INFO::Determining format of input files
2023-10-15 22:27:42.53505 INFO::Input format is data samples as rows and metadata samples as rows
2023-10-15 22:27:42.539753 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-10-15 22:27:42.541027 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-10-15 22:27:42.54348 INFO::Filter data based on min abundance and min prevalence
2023-10-15 22:27:42.544453 INFO::Total samples in data: 1595
2023-10-15 22:27:42.545315 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-10-15 22:27:42.557435 INFO::Total filtered features: 0
2023-10-15 22:27:42.558591 INFO::Filtered feature names from abundance and prevalence filtering:
2023-10-15 22:27:42.564991 INFO::Total filtered features with variance filtering: 0
2023-10-15 22:27:42.565942 INFO::Filtered feature names from variance filtering:
2023-10-15 22:27:42.566818 INFO::Running selected normalization method: TSS
2023-10-15 22:27:43.775409 INFO::Bypass z-score application to metadata
2023-10-15 22:27:43.776759 INFO::Running selected transform method: AST
2023-10-15 22:27:43.793338 INFO::Running selected analysis method: LM
2023-10-15 22:27:44.423572 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-10-15 22:27:44.779509 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-10-15 22:27:44.957238 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-10-15 22:27:45.106615 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-10-15 22:27:45.253587 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-10-15 22:27:45.395226 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-10-15 22:27:45.544007 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-10-15 22:27:45.683237 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-10-15 22:27:45.819375 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-10-15 22:27:45.949846 WARNING::Fitting problem for feature 9 a warning was issued
2023-10-15 22:27:46.095522 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-10-15 22:27:46.232017 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-10-15 22:27:46.37144 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-10-15 22:27:46.512635 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-10-15 22:27:46.63088 WARNING::Fitting problem for feature 13 a warning was issued
2023-10-15 22:27:46.799731 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-10-15 22:27:46.943296 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-10-15 22:27:47.084244 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-10-15 22:27:47.221654 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-10-15 22:27:47.387114 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-10-15 22:27:47.544592 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-10-15 22:27:47.691759 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-10-15 22:27:47.853494 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-10-15 22:27:47.994761 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-10-15 22:27:48.135019 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-10-15 22:27:48.278385 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-10-15 22:27:48.416545 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-10-15 22:27:48.557784 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-10-15 22:27:48.69744 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-10-15 22:27:48.839411 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-10-15 22:27:48.979065 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-10-15 22:27:49.125949 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-10-15 22:27:49.265403 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-10-15 22:27:49.418008 INFO::Fitting model to feature number 32, Prevotella.copri
2023-10-15 22:27:49.572905 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-10-15 22:27:49.724207 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-10-15 22:27:49.874428 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-10-15 22:27:50.019269 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-10-15 22:27:50.167632 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-10-15 22:27:50.318679 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-10-15 22:27:50.464312 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-10-15 22:27:50.605962 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-10-15 22:27:50.763103 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-10-15 22:27:50.911203 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-10-15 22:27:51.065594 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-10-15 22:27:51.208965 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-10-15 22:27:51.358143 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-10-15 22:27:51.506287 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-10-15 22:27:51.665486 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-10-15 22:27:51.826571 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-10-15 22:27:51.968568 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-10-15 22:27:52.129373 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-10-15 22:27:52.346054 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-10-15 22:27:52.492999 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-10-15 22:27:52.646526 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-10-15 22:27:52.813903 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-10-15 22:27:52.954681 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-10-15 22:27:53.109358 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-10-15 22:27:53.261671 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-10-15 22:27:53.406445 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-10-15 22:27:53.529062 WARNING::Fitting problem for feature 58 a warning was issued
2023-10-15 22:27:53.677218 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-10-15 22:27:53.824634 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-10-15 22:27:53.963046 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-10-15 22:27:54.106337 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-10-15 22:27:54.51043 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-10-15 22:27:54.648282 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-10-15 22:27:54.78713 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-10-15 22:27:54.93968 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-10-15 22:27:55.075236 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-10-15 22:27:55.208578 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-10-15 22:27:55.357386 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-10-15 22:27:55.502629 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-10-15 22:27:55.649019 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-10-15 22:27:55.796136 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-10-15 22:27:55.934438 INFO::Fitting model to feature number 73, Dialister.invisus
2023-10-15 22:27:56.07226 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-10-15 22:27:56.219352 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-10-15 22:27:56.359413 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-10-15 22:27:56.501232 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-10-15 22:27:56.651193 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-10-15 22:27:56.799248 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-10-15 22:27:56.945867 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-10-15 22:27:57.090041 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-10-15 22:27:57.234608 INFO::Fitting model to feature number 82, Escherichia.coli
2023-10-15 22:27:57.374977 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-10-15 22:27:57.514504 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-10-15 22:27:57.655226 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-10-15 22:27:57.795945 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-10-15 22:27:57.938472 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-10-15 22:27:58.153976 INFO::Counting total values for each feature
2023-10-15 22:27:58.190345 INFO::Writing filtered data to file output/features/filtered_data.tsv
2023-10-15 22:27:58.335626 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2023-10-15 22:27:58.485919 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2023-10-15 22:27:58.639172 INFO::Writing residuals to file output/fits/residuals.rds
2023-10-15 22:27:58.696581 INFO::Writing fitted values to file output/fits/fitted.rds
2023-10-15 22:27:58.728526 INFO::Writing extracted random effects to file output/fits/ranef.rds
2023-10-15 22:27:58.734478 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-10-15 22:27:58.741603 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"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2023-10-15 22:27:58.755661 INFO::Writing function arguments to log file
2023-10-15 22:27:58.761821 INFO::Verifying options selected are valid
2023-10-15 22:27:58.762904 INFO::Determining format of input files
2023-10-15 22:27:58.76402 INFO::Input format is data samples as rows and metadata samples as rows
2023-10-15 22:27:58.768942 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-10-15 22:27:58.770027 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-10-15 22:27:58.771763 INFO::Filter data based on min abundance and min prevalence
2023-10-15 22:27:58.772666 INFO::Total samples in data: 1595
2023-10-15 22:27:58.773594 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-10-15 22:27:58.777816 INFO::Total filtered features: 0
2023-10-15 22:27:58.7788 INFO::Filtered feature names from abundance and prevalence filtering:
2023-10-15 22:27:58.791353 INFO::Total filtered features with variance filtering: 0
2023-10-15 22:27:58.792467 INFO::Filtered feature names from variance filtering:
2023-10-15 22:27:58.793302 INFO::Running selected normalization method: NONE
2023-10-15 22:27:58.794137 INFO::Bypass z-score application to metadata
2023-10-15 22:27:58.794971 INFO::Running selected transform method: AST
2023-10-15 22:27:58.808609 INFO::Running selected analysis method: LM
2023-10-15 22:27:58.810173 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-10-15 22:27:58.949283 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-10-15 22:27:59.082659 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-10-15 22:27:59.222187 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-10-15 22:27:59.353701 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-10-15 22:27:59.488645 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-10-15 22:27:59.622653 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-10-15 22:27:59.760829 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-10-15 22:27:59.892801 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-10-15 22:28:00.034034 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-10-15 22:28:00.176854 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-10-15 22:28:00.322125 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-10-15 22:28:00.4833 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-10-15 22:28:00.603606 WARNING::Fitting problem for feature 13 a warning was issued
2023-10-15 22:28:00.759159 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-10-15 22:28:00.90361 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-10-15 22:28:01.039698 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-10-15 22:28:01.175221 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-10-15 22:28:01.322631 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-10-15 22:28:01.456429 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-10-15 22:28:01.585905 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-10-15 22:28:01.741912 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-10-15 22:28:01.8821 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-10-15 22:28:02.035745 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-10-15 22:28:02.167053 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-10-15 22:28:02.308861 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-10-15 22:28:02.467956 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-10-15 22:28:02.609028 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-10-15 22:28:02.761694 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-10-15 22:28:02.88932 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-10-15 22:28:03.01721 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-10-15 22:28:03.160056 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-10-15 22:28:03.294246 INFO::Fitting model to feature number 32, Prevotella.copri
2023-10-15 22:28:03.438549 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-10-15 22:28:03.580642 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-10-15 22:28:03.71709 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-10-15 22:28:03.853912 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-10-15 22:28:03.995936 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-10-15 22:28:04.129001 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-10-15 22:28:04.277394 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-10-15 22:28:04.409281 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-10-15 22:28:04.543842 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-10-15 22:28:04.686387 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-10-15 22:28:04.823143 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-10-15 22:28:04.980604 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-10-15 22:28:05.117224 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-10-15 22:28:05.265173 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-10-15 22:28:05.403549 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-10-15 22:28:05.541405 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-10-15 22:28:05.678617 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-10-15 22:28:05.81996 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-10-15 22:28:05.944869 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-10-15 22:28:06.111413 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-10-15 22:28:06.242912 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-10-15 22:28:06.38422 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-10-15 22:28:06.523234 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-10-15 22:28:06.66506 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-10-15 22:28:06.814195 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-10-15 22:28:06.945658 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-10-15 22:28:07.090228 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-10-15 22:28:07.223286 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-10-15 22:28:07.352645 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-10-15 22:28:07.495193 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-10-15 22:28:07.628124 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-10-15 22:28:07.778163 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-10-15 22:28:07.910727 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-10-15 22:28:08.044524 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-10-15 22:28:08.189247 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-10-15 22:28:08.303926 WARNING::Fitting problem for feature 67 a warning was issued
2023-10-15 22:28:08.460939 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-10-15 22:28:08.596692 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-10-15 22:28:08.740227 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-10-15 22:28:08.88512 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-10-15 22:28:09.036188 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-10-15 22:28:09.088276 WARNING::Fitting problem for feature 72 a warning was issued
2023-10-15 22:28:09.228168 INFO::Fitting model to feature number 73, Dialister.invisus
2023-10-15 22:28:09.372189 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-10-15 22:28:09.51284 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-10-15 22:28:09.644428 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-10-15 22:28:09.792235 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-10-15 22:28:09.922487 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-10-15 22:28:10.065881 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-10-15 22:28:10.214822 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-10-15 22:28:10.347152 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-10-15 22:28:10.510471 INFO::Fitting model to feature number 82, Escherichia.coli
2023-10-15 22:28:10.651087 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-10-15 22:28:10.789386 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-10-15 22:28:10.946316 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-10-15 22:28:11.081826 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-10-15 22:28:11.229705 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-10-15 22:28:11.392275 INFO::Counting total values for each feature
2023-10-15 22:28:11.42428 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2023-10-15 22:28:11.568124 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2023-10-15 22:28:11.712601 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2023-10-15 22:28:11.865017 INFO::Writing residuals to file output2/fits/residuals.rds
2023-10-15 22:28:11.940718 INFO::Writing fitted values to file output2/fits/fitted.rds
2023-10-15 22:28:12.013727 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2023-10-15 22:28:12.019891 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-10-15 22:28:12.025773 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.204   0.527  30.721