##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Maaslin2_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2023-01-10 r83596 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 88.09   6.25   94.85
* 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
  'F:/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/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 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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"
2023-03-16 03:07:46.752002 INFO::Writing function arguments to log file
2023-03-16 03:07:46.785 INFO::Verifying options selected are valid
2023-03-16 03:07:46.819337 INFO::Determining format of input files
2023-03-16 03:07:46.82166 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-16 03:07:46.828759 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-03-16 03:07:46.831077 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-03-16 03:07:46.842099 INFO::Filter data based on min abundance and min prevalence
2023-03-16 03:07:46.844263 INFO::Total samples in data: 1595
2023-03-16 03:07:46.846016 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-03-16 03:07:46.851392 INFO::Total filtered features: 0
2023-03-16 03:07:46.853417 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-16 03:07:46.862283 INFO::Total filtered features with variance filtering: 0
2023-03-16 03:07:46.864401 INFO::Filtered feature names from variance filtering:
2023-03-16 03:07:46.866191 INFO::Running selected normalization method: TSS
2023-03-16 03:07:47.998849 INFO::Bypass z-score application to metadata
2023-03-16 03:07:48.001135 INFO::Running selected transform method: AST
2023-03-16 03:07:48.018593 INFO::Running selected analysis method: LM
2023-03-16 03:07:48.5837 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-03-16 03:07:48.968462 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-03-16 03:07:49.119591 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-03-16 03:07:49.255709 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-03-16 03:07:49.395545 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-03-16 03:07:49.541458 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-03-16 03:07:49.676026 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-03-16 03:07:49.820773 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-03-16 03:07:49.989959 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-03-16 03:07:50.130322 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-03-16 03:07:50.264691 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-03-16 03:07:50.406707 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-03-16 03:07:50.547471 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-03-16 03:07:50.704564 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-03-16 03:07:50.849997 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-03-16 03:07:51.009779 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-03-16 03:07:51.147364 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-03-16 03:07:51.288081 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-03-16 03:07:51.438045 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-03-16 03:07:51.569032 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-03-16 03:07:51.702909 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-03-16 03:07:51.848424 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-03-16 03:07:51.995365 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-03-16 03:07:52.134896 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-03-16 03:07:52.279902 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-03-16 03:07:52.425468 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-03-16 03:07:52.563191 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-03-16 03:07:52.712046 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-03-16 03:07:52.850271 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-03-16 03:07:52.999062 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-03-16 03:07:53.193908 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-03-16 03:07:53.339283 INFO::Fitting model to feature number 32, Prevotella.copri
2023-03-16 03:07:53.525308 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-03-16 03:07:53.907146 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-03-16 03:07:54.042236 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-03-16 03:07:54.178515 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-03-16 03:07:54.319927 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-03-16 03:07:54.509522 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-03-16 03:07:54.670279 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-03-16 03:07:54.803157 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-03-16 03:07:54.980425 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-03-16 03:07:55.119282 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-03-16 03:07:55.282071 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-03-16 03:07:55.429882 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-03-16 03:07:55.55941 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-03-16 03:07:55.697691 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-03-16 03:07:55.850504 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-03-16 03:07:55.990712 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-03-16 03:07:56.120585 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-03-16 03:07:56.256684 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-03-16 03:07:56.384917 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-03-16 03:07:56.513154 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-03-16 03:07:56.652029 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-03-16 03:07:56.789743 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-03-16 03:07:56.95669 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-03-16 03:07:57.097923 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-03-16 03:07:57.240004 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-03-16 03:07:57.369531 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-03-16 03:07:57.500943 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-03-16 03:07:57.636239 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-03-16 03:07:57.765156 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-03-16 03:07:57.896102 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-03-16 03:07:58.035169 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-03-16 03:07:58.230787 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-03-16 03:07:58.410809 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-03-16 03:07:58.535576 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-03-16 03:07:58.66941 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-03-16 03:07:58.791099 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-03-16 03:07:58.929342 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-03-16 03:07:59.092444 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-03-16 03:07:59.232426 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-03-16 03:07:59.361832 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-03-16 03:07:59.738569 INFO::Fitting model to feature number 73, Dialister.invisus
2023-03-16 03:07:59.867227 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-03-16 03:08:00.028693 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-03-16 03:08:00.168889 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-03-16 03:08:00.327334 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-03-16 03:08:00.464211 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-03-16 03:08:00.61565 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-03-16 03:08:00.759565 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-03-16 03:08:00.915665 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-03-16 03:08:01.086119 INFO::Fitting model to feature number 82, Escherichia.coli
2023-03-16 03:08:01.233025 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-03-16 03:08:01.376388 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-03-16 03:08:01.516934 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-03-16 03:08:01.674872 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-03-16 03:08:01.826049 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-03-16 03:08:02.010536 INFO::Counting total values for each feature
2023-03-16 03:08:02.044636 INFO::Writing residuals to file output/residuals.rds
2023-03-16 03:08:02.090722 INFO::Writing fitted values to file output/fitted.rds
2023-03-16 03:08:02.114254 INFO::Writing extracted random effects to file output/ranef.rds
2023-03-16 03:08:02.120858 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-03-16 03:08:02.135779 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"
2023-03-16 03:08:02.160419 INFO::Writing function arguments to log file
2023-03-16 03:08:02.176902 INFO::Verifying options selected are valid
2023-03-16 03:08:02.178944 INFO::Determining format of input files
2023-03-16 03:08:02.181093 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-16 03:08:02.188765 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-03-16 03:08:02.190887 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-03-16 03:08:02.198606 INFO::Filter data based on min abundance and min prevalence
2023-03-16 03:08:02.20074 INFO::Total samples in data: 1595
2023-03-16 03:08:02.203526 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-03-16 03:08:02.223645 INFO::Total filtered features: 0
2023-03-16 03:08:02.227206 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-16 03:08:02.235287 INFO::Total filtered features with variance filtering: 0
2023-03-16 03:08:02.237855 INFO::Filtered feature names from variance filtering:
2023-03-16 03:08:02.239584 INFO::Running selected normalization method: NONE
2023-03-16 03:08:02.241241 INFO::Bypass z-score application to metadata
2023-03-16 03:08:02.24299 INFO::Running selected transform method: AST
2023-03-16 03:08:02.255584 INFO::Running selected analysis method: LM
2023-03-16 03:08:02.258574 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-03-16 03:08:02.395978 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-03-16 03:08:02.528571 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-03-16 03:08:02.667521 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-03-16 03:08:02.79579 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-03-16 03:08:02.934453 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-03-16 03:08:03.094027 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-03-16 03:08:03.232809 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-03-16 03:08:03.360215 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-03-16 03:08:03.495775 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-03-16 03:08:03.629428 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-03-16 03:08:03.783428 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-03-16 03:08:03.913877 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-03-16 03:08:04.052635 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-03-16 03:08:04.179953 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-03-16 03:08:04.32232 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-03-16 03:08:04.460812 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-03-16 03:08:04.592563 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-03-16 03:08:04.733856 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-03-16 03:08:04.859281 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-03-16 03:08:05.011 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-03-16 03:08:05.145942 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-03-16 03:08:05.28382 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-03-16 03:08:05.409891 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-03-16 03:08:05.62206 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-03-16 03:08:05.817408 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-03-16 03:08:06.026333 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-03-16 03:08:06.231177 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-03-16 03:08:06.376915 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-03-16 03:08:06.497503 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-03-16 03:08:06.621994 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-03-16 03:08:06.753669 INFO::Fitting model to feature number 32, Prevotella.copri
2023-03-16 03:08:06.883671 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-03-16 03:08:07.032884 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-03-16 03:08:07.170009 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-03-16 03:08:07.302015 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-03-16 03:08:07.435301 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-03-16 03:08:07.575355 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-03-16 03:08:07.715568 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-03-16 03:08:07.840389 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-03-16 03:08:08.012981 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-03-16 03:08:08.178291 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-03-16 03:08:08.315389 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-03-16 03:08:08.448988 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-03-16 03:08:08.58044 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-03-16 03:08:08.713706 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-03-16 03:08:08.847025 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-03-16 03:08:08.995353 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-03-16 03:08:09.201422 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-03-16 03:08:09.333944 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-03-16 03:08:09.451579 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-03-16 03:08:09.599527 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-03-16 03:08:09.716492 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-03-16 03:08:09.834941 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-03-16 03:08:09.972167 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-03-16 03:08:10.101539 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-03-16 03:08:10.237913 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-03-16 03:08:10.363879 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-03-16 03:08:10.488541 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-03-16 03:08:10.617446 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-03-16 03:08:10.752279 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-03-16 03:08:10.876975 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-03-16 03:08:11.030156 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-03-16 03:08:11.187824 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-03-16 03:08:11.369972 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-03-16 03:08:11.576374 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-03-16 03:08:11.724182 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-03-16 03:08:11.858065 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-03-16 03:08:12.017483 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-03-16 03:08:12.165113 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-03-16 03:08:12.315071 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-03-16 03:08:12.474736 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-03-16 03:08:12.615065 INFO::Fitting model to feature number 73, Dialister.invisus
2023-03-16 03:08:12.742931 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-03-16 03:08:12.870082 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-03-16 03:08:13.019297 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-03-16 03:08:13.160229 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-03-16 03:08:13.293265 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-03-16 03:08:13.426818 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-03-16 03:08:13.570207 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-03-16 03:08:13.69749 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-03-16 03:08:13.828264 INFO::Fitting model to feature number 82, Escherichia.coli
2023-03-16 03:08:13.960967 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-03-16 03:08:14.161309 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-03-16 03:08:14.365807 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-03-16 03:08:14.570392 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-03-16 03:08:14.816983 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-03-16 03:08:14.985401 INFO::Counting total values for each feature
2023-03-16 03:08:15.01189 INFO::Writing residuals to file output2/residuals.rds
2023-03-16 03:08:15.070017 INFO::Writing fitted values to file output2/fitted.rds
2023-03-16 03:08:15.123796 INFO::Writing extracted random effects to file output2/ranef.rds
2023-03-16 03:08:15.130331 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-03-16 03:08:15.141673 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 
  29.00    0.68   29.70