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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Maaslin2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 109.332  2.311 172.349
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Maaslin2.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 1.5.4
Current Matrix version is 1.5.4.1
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
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.3
Current TMB version is 1.9.4
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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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"
2023-10-18 04:17:15.196303 INFO::Writing function arguments to log file
2023-10-18 04:17:15.257647 INFO::Verifying options selected are valid
2023-10-18 04:17:15.333243 INFO::Determining format of input files
2023-10-18 04:17:15.335245 INFO::Input format is data samples as rows and metadata samples as rows
2023-10-18 04:17:15.347339 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-10-18 04:17:15.351749 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-10-18 04:17:15.35717 INFO::Filter data based on min abundance and min prevalence
2023-10-18 04:17:15.358658 INFO::Total samples in data: 1595
2023-10-18 04:17:15.35991 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-10-18 04:17:15.369375 INFO::Total filtered features: 0
2023-10-18 04:17:15.371027 INFO::Filtered feature names from abundance and prevalence filtering:
2023-10-18 04:17:15.402036 INFO::Total filtered features with variance filtering: 0
2023-10-18 04:17:15.407092 INFO::Filtered feature names from variance filtering:
2023-10-18 04:17:15.40871 INFO::Running selected normalization method: TSS
2023-10-18 04:17:17.600029 INFO::Bypass z-score application to metadata
2023-10-18 04:17:17.60531 INFO::Running selected transform method: AST
2023-10-18 04:17:17.630894 INFO::Running selected analysis method: LM
2023-10-18 04:17:18.616129 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-10-18 04:17:19.411518 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-10-18 04:17:19.75402 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-10-18 04:17:20.075833 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-10-18 04:17:20.39813 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-10-18 04:17:20.727551 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-10-18 04:17:21.023413 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-10-18 04:17:21.34311 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-10-18 04:17:21.576008 WARNING::Fitting problem for feature 8 a warning was issued
2023-10-18 04:17:21.89929 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-10-18 04:17:22.200386 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-10-18 04:17:22.488834 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-10-18 04:17:22.865756 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-10-18 04:17:23.147087 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-10-18 04:17:23.405147 WARNING::Fitting problem for feature 13 a warning was issued
2023-10-18 04:17:23.787933 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-10-18 04:17:24.074368 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-10-18 04:17:24.361857 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-10-18 04:17:24.644383 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-10-18 04:17:24.961522 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-10-18 04:17:25.267164 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-10-18 04:17:25.551857 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-10-18 04:17:25.864982 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-10-18 04:17:26.165093 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-10-18 04:17:26.478264 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-10-18 04:17:26.79059 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-10-18 04:17:27.079638 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-10-18 04:17:27.375213 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-10-18 04:17:27.681361 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-10-18 04:17:27.995339 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-10-18 04:17:28.27966 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-10-18 04:17:28.599196 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-10-18 04:17:28.885738 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-10-18 04:17:29.190959 INFO::Fitting model to feature number 32, Prevotella.copri
2023-10-18 04:17:29.49229 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-10-18 04:17:29.793557 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-10-18 04:17:30.108738 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-10-18 04:17:30.406259 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-10-18 04:17:30.690482 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-10-18 04:17:30.997843 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-10-18 04:17:31.28876 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-10-18 04:17:31.587503 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-10-18 04:17:31.919338 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-10-18 04:17:32.221502 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-10-18 04:17:32.543601 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-10-18 04:17:32.833035 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-10-18 04:17:33.127272 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-10-18 04:17:33.445248 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-10-18 04:17:33.738194 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-10-18 04:17:34.059852 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-10-18 04:17:34.362039 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-10-18 04:17:34.678953 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-10-18 04:17:34.973878 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-10-18 04:17:35.275517 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-10-18 04:17:35.577671 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-10-18 04:17:35.909255 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-10-18 04:17:36.207744 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-10-18 04:17:36.555805 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-10-18 04:17:36.895612 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-10-18 04:17:37.190241 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-10-18 04:17:37.505879 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-10-18 04:17:37.797497 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-10-18 04:17:38.099522 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-10-18 04:17:38.725401 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-10-18 04:17:39.022773 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-10-18 04:17:39.320462 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-10-18 04:17:39.60649 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-10-18 04:17:39.922409 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-10-18 04:17:40.22154 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-10-18 04:17:40.44908 WARNING::Fitting problem for feature 67 a warning was issued
2023-10-18 04:17:40.744443 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-10-18 04:17:41.056893 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-10-18 04:17:41.403459 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-10-18 04:17:41.698796 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-10-18 04:17:41.985328 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-10-18 04:17:42.278807 INFO::Fitting model to feature number 73, Dialister.invisus
2023-10-18 04:17:42.579305 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-10-18 04:17:42.874621 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-10-18 04:17:43.165252 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-10-18 04:17:43.459885 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-10-18 04:17:43.749475 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-10-18 04:17:44.078648 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-10-18 04:17:44.38777 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-10-18 04:17:44.680031 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-10-18 04:17:44.993991 INFO::Fitting model to feature number 82, Escherichia.coli
2023-10-18 04:17:45.311981 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-10-18 04:17:45.616199 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-10-18 04:17:45.910363 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-10-18 04:17:46.207492 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-10-18 04:17:46.510867 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-10-18 04:17:46.888362 INFO::Counting total values for each feature
2023-10-18 04:17:46.941458 INFO::Writing filtered data to file output/features/filtered_data.tsv
2023-10-18 04:17:47.161654 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2023-10-18 04:17:47.424721 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2023-10-18 04:17:47.699495 INFO::Writing residuals to file output/fits/residuals.rds
2023-10-18 04:17:47.808608 INFO::Writing fitted values to file output/fits/fitted.rds
2023-10-18 04:17:47.86826 INFO::Writing extracted random effects to file output/fits/ranef.rds
2023-10-18 04:17:47.881872 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-10-18 04:17:47.896723 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"
2023-10-18 04:17:47.921279 INFO::Writing function arguments to log file
2023-10-18 04:17:47.936064 INFO::Verifying options selected are valid
2023-10-18 04:17:47.940499 INFO::Determining format of input files
2023-10-18 04:17:47.94244 INFO::Input format is data samples as rows and metadata samples as rows
2023-10-18 04:17:47.955065 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-10-18 04:17:47.959022 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-10-18 04:17:47.961673 INFO::Filter data based on min abundance and min prevalence
2023-10-18 04:17:47.963851 INFO::Total samples in data: 1595
2023-10-18 04:17:47.970638 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-10-18 04:17:47.996316 INFO::Total filtered features: 0
2023-10-18 04:17:47.998043 INFO::Filtered feature names from abundance and prevalence filtering:
2023-10-18 04:17:48.012371 INFO::Total filtered features with variance filtering: 0
2023-10-18 04:17:48.014245 INFO::Filtered feature names from variance filtering:
2023-10-18 04:17:48.01959 INFO::Running selected normalization method: NONE
2023-10-18 04:17:48.021106 INFO::Bypass z-score application to metadata
2023-10-18 04:17:48.022418 INFO::Running selected transform method: AST
2023-10-18 04:17:48.047968 INFO::Running selected analysis method: LM
2023-10-18 04:17:48.050321 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-10-18 04:17:48.33449 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-10-18 04:17:48.624317 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-10-18 04:17:48.936742 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-10-18 04:17:49.216376 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-10-18 04:17:49.50274 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-10-18 04:17:49.783138 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-10-18 04:17:50.060131 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-10-18 04:17:50.332898 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-10-18 04:17:50.554023 WARNING::Fitting problem for feature 9 a warning was issued
2023-10-18 04:17:50.860469 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-10-18 04:17:51.141413 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-10-18 04:17:51.423049 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-10-18 04:17:51.698679 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-10-18 04:17:51.9951 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-10-18 04:17:52.263732 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-10-18 04:17:52.54764 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-10-18 04:17:52.835678 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-10-18 04:17:53.134698 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-10-18 04:17:53.419227 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-10-18 04:17:53.699954 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-10-18 04:17:54.023402 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-10-18 04:17:54.288051 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-10-18 04:17:54.552184 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-10-18 04:17:54.810538 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-10-18 04:17:55.074797 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-10-18 04:17:55.351932 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-10-18 04:17:55.639817 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-10-18 04:17:55.896363 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-10-18 04:17:56.183981 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-10-18 04:17:56.451947 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-10-18 04:17:56.713932 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-10-18 04:17:56.979265 INFO::Fitting model to feature number 32, Prevotella.copri
2023-10-18 04:17:57.248301 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-10-18 04:17:57.492443 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-10-18 04:17:57.760738 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-10-18 04:17:58.057673 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-10-18 04:17:58.356551 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-10-18 04:17:58.634455 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-10-18 04:17:58.91946 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-10-18 04:17:59.190151 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-10-18 04:17:59.817145 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-10-18 04:18:00.104442 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-10-18 04:18:00.410611 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-10-18 04:18:00.743413 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-10-18 04:18:01.0695 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-10-18 04:18:01.363383 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-10-18 04:18:01.655061 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-10-18 04:18:01.911666 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-10-18 04:18:02.186732 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-10-18 04:18:02.480156 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-10-18 04:18:02.73228 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-10-18 04:18:03.018446 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-10-18 04:18:03.280448 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-10-18 04:18:03.549944 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-10-18 04:18:03.833454 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-10-18 04:18:04.112025 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-10-18 04:18:04.38659 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-10-18 04:18:04.663426 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-10-18 04:18:04.931006 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-10-18 04:18:05.244524 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-10-18 04:18:05.519489 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-10-18 04:18:05.80655 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-10-18 04:18:06.089371 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-10-18 04:18:06.389732 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-10-18 04:18:06.671832 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-10-18 04:18:06.926987 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-10-18 04:18:07.185803 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-10-18 04:18:07.454518 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-10-18 04:18:07.732543 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-10-18 04:18:08.014428 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-10-18 04:18:08.329999 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-10-18 04:18:08.607566 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-10-18 04:18:08.701621 WARNING::Fitting problem for feature 72 a warning was issued
2023-10-18 04:18:09.31816 INFO::Fitting model to feature number 73, Dialister.invisus
2023-10-18 04:18:09.598858 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-10-18 04:18:09.903067 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-10-18 04:18:10.188029 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-10-18 04:18:10.508713 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-10-18 04:18:10.79813 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-10-18 04:18:11.072969 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-10-18 04:18:11.350887 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-10-18 04:18:11.644819 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-10-18 04:18:11.932933 INFO::Fitting model to feature number 82, Escherichia.coli
2023-10-18 04:18:12.187695 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-10-18 04:18:12.458787 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-10-18 04:18:12.725186 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-10-18 04:18:13.019141 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-10-18 04:18:13.337115 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-10-18 04:18:13.68379 INFO::Counting total values for each feature
2023-10-18 04:18:13.722466 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2023-10-18 04:18:13.93301 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2023-10-18 04:18:14.159583 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2023-10-18 04:18:14.419905 INFO::Writing residuals to file output2/fits/residuals.rds
2023-10-18 04:18:14.564998 INFO::Writing fitted values to file output2/fits/fitted.rds
2023-10-18 04:18:14.708251 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2023-10-18 04:18:14.721685 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-10-18 04:18:14.733716 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 39.111   0.886  61.936