##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* 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 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 174.957  1.702 233.201
* 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/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/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.1
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-apple-darwin17.0 (64-bit)

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

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

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

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
2023-03-16 03:14:52.951636 INFO::Writing function arguments to log file
2023-03-16 03:14:53.03735 INFO::Verifying options selected are valid
2023-03-16 03:14:53.146211 INFO::Determining format of input files
2023-03-16 03:14:53.149044 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-16 03:14:53.167325 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-03-16 03:14:53.17028 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-03-16 03:14:53.175301 INFO::Filter data based on min abundance and min prevalence
2023-03-16 03:14:53.180514 INFO::Total samples in data: 1595
2023-03-16 03:14:53.182478 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-03-16 03:14:53.194956 INFO::Total filtered features: 0
2023-03-16 03:14:53.19741 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-16 03:14:53.238942 INFO::Total filtered features with variance filtering: 0
2023-03-16 03:14:53.241382 INFO::Filtered feature names from variance filtering:
2023-03-16 03:14:53.247317 INFO::Running selected normalization method: TSS
2023-03-16 03:14:56.454377 INFO::Bypass z-score application to metadata
2023-03-16 03:14:56.459565 INFO::Running selected transform method: AST
2023-03-16 03:14:56.5032 INFO::Running selected analysis method: LM
2023-03-16 03:14:57.859968 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-03-16 03:14:59.044162 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-03-16 03:14:59.509524 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-03-16 03:14:59.926407 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-03-16 03:15:00.338999 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-03-16 03:15:00.756706 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-03-16 03:15:01.165355 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-03-16 03:15:01.562952 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-03-16 03:15:01.980083 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-03-16 03:15:02.365063 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-03-16 03:15:02.749378 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-03-16 03:15:03.135837 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-03-16 03:15:03.611665 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-03-16 03:15:04.055965 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-03-16 03:15:04.439653 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-03-16 03:15:04.854098 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-03-16 03:15:05.252811 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-03-16 03:15:05.661087 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-03-16 03:15:06.083002 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-03-16 03:15:06.48606 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-03-16 03:15:06.890424 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-03-16 03:15:07.298837 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-03-16 03:15:07.71221 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-03-16 03:15:08.121507 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-03-16 03:15:08.552095 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-03-16 03:15:08.983961 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-03-16 03:15:09.413698 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-03-16 03:15:09.839474 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-03-16 03:15:10.258578 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-03-16 03:15:10.682227 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-03-16 03:15:11.065573 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-03-16 03:15:11.49611 INFO::Fitting model to feature number 32, Prevotella.copri
2023-03-16 03:15:11.889857 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-03-16 03:15:12.31896 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-03-16 03:15:12.737917 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-03-16 03:15:13.142053 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-03-16 03:15:13.559054 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-03-16 03:15:13.960167 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-03-16 03:15:14.370062 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-03-16 03:15:14.780663 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-03-16 03:15:15.189576 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-03-16 03:15:15.601423 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-03-16 03:15:16.00407 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-03-16 03:15:16.389222 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-03-16 03:15:16.795362 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-03-16 03:15:17.194157 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-03-16 03:15:17.601378 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-03-16 03:15:18.006392 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-03-16 03:15:18.404523 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-03-16 03:15:18.82037 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-03-16 03:15:19.218713 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-03-16 03:15:19.629082 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-03-16 03:15:20.054281 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-03-16 03:15:20.476775 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-03-16 03:15:20.866289 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-03-16 03:15:21.269264 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-03-16 03:15:21.70757 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-03-16 03:15:22.457272 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-03-16 03:15:22.870636 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-03-16 03:15:23.257694 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-03-16 03:15:23.65792 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-03-16 03:15:24.051406 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-03-16 03:15:24.452724 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-03-16 03:15:25.196693 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-03-16 03:15:25.56259 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-03-16 03:15:25.929241 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-03-16 03:15:26.325731 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-03-16 03:15:26.782868 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-03-16 03:15:27.166758 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-03-16 03:15:27.572413 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-03-16 03:15:27.981321 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-03-16 03:15:28.374441 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-03-16 03:15:28.794352 INFO::Fitting model to feature number 73, Dialister.invisus
2023-03-16 03:15:29.185397 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-03-16 03:15:29.608415 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-03-16 03:15:30.048546 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-03-16 03:15:30.461748 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-03-16 03:15:30.854156 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-03-16 03:15:31.2615 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-03-16 03:15:31.67528 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-03-16 03:15:32.078113 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-03-16 03:15:32.520513 INFO::Fitting model to feature number 82, Escherichia.coli
2023-03-16 03:15:32.917694 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-03-16 03:15:33.307952 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-03-16 03:15:33.699728 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-03-16 03:15:34.112876 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-03-16 03:15:34.491154 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-03-16 03:15:35.036901 INFO::Counting total values for each feature
2023-03-16 03:15:35.14933 INFO::Writing residuals to file output/residuals.rds
2023-03-16 03:15:35.264836 INFO::Writing fitted values to file output/fitted.rds
2023-03-16 03:15:35.339741 INFO::Writing extracted random effects to file output/ranef.rds
2023-03-16 03:15:35.355412 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-03-16 03:15:35.374313 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 03:15:35.405531 INFO::Writing function arguments to log file
2023-03-16 03:15:35.424822 INFO::Verifying options selected are valid
2023-03-16 03:15:35.427079 INFO::Determining format of input files
2023-03-16 03:15:35.429635 INFO::Input format is data samples as rows and metadata samples as rows
2023-03-16 03:15:35.444503 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-03-16 03:15:35.450828 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-03-16 03:15:35.46687 INFO::Filter data based on min abundance and min prevalence
2023-03-16 03:15:35.469077 INFO::Total samples in data: 1595
2023-03-16 03:15:35.47106 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-03-16 03:15:35.483898 INFO::Total filtered features: 0
2023-03-16 03:15:35.488322 INFO::Filtered feature names from abundance and prevalence filtering:
2023-03-16 03:15:35.509398 INFO::Total filtered features with variance filtering: 0
2023-03-16 03:15:35.53102 INFO::Filtered feature names from variance filtering:
2023-03-16 03:15:35.533819 INFO::Running selected normalization method: NONE
2023-03-16 03:15:35.536012 INFO::Bypass z-score application to metadata
2023-03-16 03:15:35.542766 INFO::Running selected transform method: AST
2023-03-16 03:15:35.580565 INFO::Running selected analysis method: LM
2023-03-16 03:15:35.584855 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-03-16 03:15:35.962714 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-03-16 03:15:36.348954 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-03-16 03:15:36.711174 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-03-16 03:15:37.11437 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-03-16 03:15:37.476396 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-03-16 03:15:37.850257 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-03-16 03:15:38.227702 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-03-16 03:15:38.614964 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-03-16 03:15:39.015862 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-03-16 03:15:39.400757 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-03-16 03:15:39.794931 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-03-16 03:15:40.213786 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-03-16 03:15:40.595936 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-03-16 03:15:40.951645 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-03-16 03:15:41.318093 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-03-16 03:15:41.705087 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-03-16 03:15:42.10996 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-03-16 03:15:42.4752 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-03-16 03:15:42.846952 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-03-16 03:15:43.25294 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-03-16 03:15:43.649842 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-03-16 03:15:44.005218 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-03-16 03:15:44.349033 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-03-16 03:15:44.741627 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-03-16 03:15:45.118361 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-03-16 03:15:45.481982 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-03-16 03:15:45.86788 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-03-16 03:15:46.236707 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-03-16 03:15:46.58284 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-03-16 03:15:46.934908 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-03-16 03:15:47.309027 INFO::Fitting model to feature number 32, Prevotella.copri
2023-03-16 03:15:47.696285 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-03-16 03:15:48.048764 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-03-16 03:15:48.423746 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-03-16 03:15:48.798294 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-03-16 03:15:49.166851 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-03-16 03:15:49.52621 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-03-16 03:15:49.923009 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-03-16 03:15:50.31822 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-03-16 03:15:50.675272 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-03-16 03:15:51.056966 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-03-16 03:15:51.467467 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-03-16 03:15:51.861868 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-03-16 03:15:52.243325 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-03-16 03:15:52.639098 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-03-16 03:15:53.022109 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-03-16 03:15:53.374223 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-03-16 03:15:53.753069 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-03-16 03:15:54.118235 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-03-16 03:15:54.49152 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-03-16 03:15:54.888847 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-03-16 03:15:55.230782 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-03-16 03:15:55.588788 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-03-16 03:15:55.959236 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-03-16 03:15:56.335833 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-03-16 03:15:56.749921 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-03-16 03:15:57.118471 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-03-16 03:15:57.487786 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-03-16 03:15:57.880267 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-03-16 03:15:58.226318 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-03-16 03:15:58.615326 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-03-16 03:15:58.993914 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-03-16 03:15:59.379809 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-03-16 03:15:59.780146 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-03-16 03:16:00.167901 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-03-16 03:16:00.549511 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-03-16 03:16:00.955094 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-03-16 03:16:01.327027 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-03-16 03:16:01.71707 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-03-16 03:16:02.111823 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-03-16 03:16:02.495756 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-03-16 03:16:02.911084 INFO::Fitting model to feature number 73, Dialister.invisus
2023-03-16 03:16:03.285698 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-03-16 03:16:03.670141 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-03-16 03:16:04.039943 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-03-16 03:16:04.436747 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-03-16 03:16:04.818172 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-03-16 03:16:05.210837 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-03-16 03:16:05.629613 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-03-16 03:16:06.025556 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-03-16 03:16:06.392883 INFO::Fitting model to feature number 82, Escherichia.coli
2023-03-16 03:16:06.763106 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-03-16 03:16:07.120283 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-03-16 03:16:07.480326 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-03-16 03:16:07.846372 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-03-16 03:16:08.244346 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-03-16 03:16:08.760367 INFO::Counting total values for each feature
2023-03-16 03:16:08.838051 INFO::Writing residuals to file output2/residuals.rds
2023-03-16 03:16:09.028689 INFO::Writing fitted values to file output2/fitted.rds
2023-03-16 03:16:09.188757 INFO::Writing extracted random effects to file output2/ranef.rds
2023-03-16 03:16:09.20256 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-03-16 03:16:09.219997 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 59.437   0.754  79.594