##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* 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 code 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 120.736  0.834 121.845
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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"
2024-05-09 08:58:57.022332 INFO::Writing function arguments to log file
2024-05-09 08:58:57.077537 INFO::Verifying options selected are valid
2024-05-09 08:58:57.122209 INFO::Determining format of input files
2024-05-09 08:58:57.124047 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-09 08:58:57.131319 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-09 08:58:57.133172 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-09 08:58:57.136595 INFO::Filter data based on min abundance and min prevalence
2024-05-09 08:58:57.138003 INFO::Total samples in data: 1595
2024-05-09 08:58:57.13925 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-09 08:58:57.150132 INFO::Total filtered features: 0
2024-05-09 08:58:57.15173 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-09 08:58:57.193071 INFO::Total filtered features with variance filtering: 0
2024-05-09 08:58:57.19461 INFO::Filtered feature names from variance filtering:
2024-05-09 08:58:57.195855 INFO::Running selected normalization method: TSS
2024-05-09 08:58:58.688774 INFO::Bypass z-score application to metadata
2024-05-09 08:58:58.690314 INFO::Running selected transform method: AST
2024-05-09 08:58:58.715519 INFO::Running selected analysis method: LM
2024-05-09 08:58:59.364537 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-09 08:58:59.848228 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-09 08:59:00.092035 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-09 08:59:00.340055 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-09 08:59:00.869757 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-09 08:59:01.109364 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-09 08:59:01.348886 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-09 08:59:01.596431 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-09 08:59:01.808001 WARNING::Fitting problem for feature 8 a warning was issued
2024-05-09 08:59:02.067462 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-09 08:59:02.263437 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-09 08:59:02.540175 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-09 08:59:02.778867 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-09 08:59:03.017005 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-09 08:59:03.261235 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-09 08:59:03.459788 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-09 08:59:03.71367 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-09 08:59:03.966738 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-09 08:59:04.252579 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-09 08:59:04.496343 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-09 08:59:04.764102 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-09 08:59:05.025437 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-09 08:59:05.250046 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-09 08:59:05.495125 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-09 08:59:05.751123 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-09 08:59:06.017539 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-09 08:59:06.260427 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-09 08:59:06.546372 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-09 08:59:06.821874 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-09 08:59:07.064412 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-09 08:59:07.32863 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-09 08:59:07.591402 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-09 08:59:07.837982 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-09 08:59:08.069744 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-09 08:59:08.319279 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-09 08:59:08.575004 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-09 08:59:08.834275 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-09 08:59:09.08048 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-09 08:59:09.299903 WARNING::Fitting problem for feature 35 a warning was issued
2024-05-09 08:59:09.56403 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-09 08:59:09.8163 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-09 08:59:10.079798 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-09 08:59:10.320602 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-09 08:59:10.556824 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-09 08:59:10.811811 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-09 08:59:11.055018 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-09 08:59:11.316481 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-09 08:59:11.558432 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-09 08:59:11.801116 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-09 08:59:12.063402 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-09 08:59:12.333247 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-09 08:59:12.606958 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-09 08:59:12.848507 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-09 08:59:13.086291 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-09 08:59:13.335474 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-09 08:59:13.577677 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-09 08:59:13.838231 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-09 08:59:14.097971 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-09 08:59:14.35189 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-09 08:59:14.607067 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-09 08:59:14.875011 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-09 08:59:15.106836 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-09 08:59:15.367442 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-09 08:59:15.606715 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-09 08:59:15.861945 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-09 08:59:16.111795 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-09 08:59:16.376871 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-09 08:59:16.642714 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-09 08:59:16.894785 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-09 08:59:17.141981 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-09 08:59:17.403802 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-09 08:59:17.64147 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-09 08:59:18.186326 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-09 08:59:18.443821 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-09 08:59:18.70379 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-09 08:59:18.965699 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-09 08:59:19.208405 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-09 08:59:19.447865 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-09 08:59:19.704175 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-09 08:59:19.954216 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-09 08:59:20.213867 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-09 08:59:20.48357 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-09 08:59:20.760447 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-09 08:59:21.032876 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-09 08:59:21.297151 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-09 08:59:21.554393 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-09 08:59:21.807928 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-09 08:59:22.067124 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-09 08:59:22.304792 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-09 08:59:22.535561 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-09 08:59:22.77583 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-09 08:59:23.073865 INFO::Counting total values for each feature
2024-05-09 08:59:23.138586 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-09 08:59:23.264647 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-09 08:59:23.391899 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-09 08:59:23.522089 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-09 08:59:23.572793 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-09 08:59:23.59976 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-09 08:59:23.605843 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-09 08:59:23.61257 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"
2024-05-09 08:59:23.629614 INFO::Writing function arguments to log file
2024-05-09 08:59:23.637677 INFO::Verifying options selected are valid
2024-05-09 08:59:23.639034 INFO::Determining format of input files
2024-05-09 08:59:23.640535 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-09 08:59:23.647886 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-09 08:59:23.649514 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-09 08:59:23.651843 INFO::Filter data based on min abundance and min prevalence
2024-05-09 08:59:23.653125 INFO::Total samples in data: 1595
2024-05-09 08:59:23.654325 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-09 08:59:23.664671 INFO::Total filtered features: 0
2024-05-09 08:59:23.666164 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-09 08:59:23.69724 INFO::Total filtered features with variance filtering: 0
2024-05-09 08:59:23.698746 INFO::Filtered feature names from variance filtering:
2024-05-09 08:59:23.699955 INFO::Running selected normalization method: NONE
2024-05-09 08:59:23.701062 INFO::Bypass z-score application to metadata
2024-05-09 08:59:23.702196 INFO::Running selected transform method: AST
2024-05-09 08:59:23.734813 INFO::Running selected analysis method: LM
2024-05-09 08:59:23.737417 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-09 08:59:23.960084 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-09 08:59:24.196084 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-09 08:59:24.429485 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-09 08:59:24.653679 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-09 08:59:24.876698 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-09 08:59:25.10793 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-09 08:59:25.355252 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-09 08:59:25.59125 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-09 08:59:25.833337 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-09 08:59:26.072262 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-09 08:59:26.29933 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-09 08:59:26.517007 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-09 08:59:26.750128 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-09 08:59:26.975839 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-09 08:59:27.216369 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-09 08:59:27.392769 WARNING::Fitting problem for feature 16 a warning was issued
2024-05-09 08:59:27.622087 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-09 08:59:27.86529 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-09 08:59:28.09079 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-09 08:59:28.306863 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-09 08:59:28.549345 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-09 08:59:28.778157 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-09 08:59:29.025716 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-09 08:59:29.239489 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-09 08:59:29.466943 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-09 08:59:29.702338 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-09 08:59:29.924505 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-09 08:59:30.166523 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-09 08:59:30.386387 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-09 08:59:30.641261 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-09 08:59:30.867668 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-09 08:59:31.101916 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-09 08:59:31.339599 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-09 08:59:31.57691 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-09 08:59:31.806065 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-09 08:59:32.047796 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-09 08:59:32.273292 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-09 08:59:32.503126 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-09 08:59:32.748437 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-09 08:59:32.96295 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-09 08:59:33.178383 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-09 08:59:33.416352 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-09 08:59:33.64128 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-09 08:59:33.877731 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-09 08:59:34.127759 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-09 08:59:34.361203 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-09 08:59:34.60828 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-09 08:59:34.820728 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-09 08:59:35.042008 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-09 08:59:35.272286 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-09 08:59:35.481558 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-09 08:59:35.721181 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-09 08:59:35.936485 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-09 08:59:36.162994 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-09 08:59:36.379537 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-09 08:59:36.611249 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-09 08:59:36.836097 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-09 08:59:37.067504 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-09 08:59:37.28784 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-09 08:59:37.527565 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-09 08:59:37.749756 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-09 08:59:37.994447 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-09 08:59:38.2084 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-09 08:59:38.444998 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-09 08:59:38.692775 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-09 08:59:38.920991 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-09 08:59:39.148639 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-09 08:59:39.344783 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-09 08:59:39.575643 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-09 08:59:39.789483 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-09 08:59:40.033879 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-09 08:59:40.272841 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-09 08:59:40.509526 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-09 08:59:40.587621 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-09 08:59:40.810052 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-09 08:59:41.058341 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-09 08:59:41.290404 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-09 08:59:41.543664 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-09 08:59:41.797259 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-09 08:59:42.013435 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-09 08:59:42.250167 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-09 08:59:42.475567 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-09 08:59:42.705023 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-09 08:59:42.934377 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-09 08:59:43.160008 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-09 08:59:43.367526 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-09 08:59:43.604789 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-09 08:59:43.835113 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-09 08:59:44.093987 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-09 08:59:44.356511 INFO::Counting total values for each feature
2024-05-09 08:59:44.394725 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-09 08:59:44.519305 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-09 08:59:44.644078 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-09 08:59:44.784761 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-09 08:59:44.850214 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-09 08:59:44.913752 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-09 08:59:44.920171 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-09 08:59:44.926525 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 48.915   0.419  49.428