Multiple platform build/check report for BioC 3.20 - CHECK results for Maaslin2 on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for Maaslin2 on palomino8

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: Maaslin2

Version: 1.20.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz

StartedAt: 2024-12-20 03:00:37 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 03:04:07 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 209.0 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.20.0'
* 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 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 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 110.03   7.58  118.16
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2024-12-20 03:03:17.703071 INFO::Writing function arguments to log file
2024-12-20 03:03:17.765514 INFO::Verifying options selected are valid
2024-12-20 03:03:17.884507 INFO::Determining format of input files
2024-12-20 03:03:17.888067 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-20 03:03:17.899561 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-20 03:03:17.902969 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-12-20 03:03:17.907972 INFO::Filter data based on min abundance and min prevalence
2024-12-20 03:03:17.910579 INFO::Total samples in data: 1595
2024-12-20 03:03:17.92361 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-20 03:03:17.931282 INFO::Total filtered features: 0
2024-12-20 03:03:17.934271 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-20 03:03:17.94952 INFO::Total filtered features with variance filtering: 0
2024-12-20 03:03:17.952583 INFO::Filtered feature names from variance filtering:
2024-12-20 03:03:17.955265 INFO::Running selected normalization method: TSS
2024-12-20 03:03:19.653359 INFO::Bypass z-score application to metadata
2024-12-20 03:03:19.656454 INFO::Running selected transform method: AST
2024-12-20 03:03:19.679655 INFO::Running selected analysis method: LM
2024-12-20 03:03:20.126888 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-20 03:03:20.822612 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-20 03:03:20.991384 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-20 03:03:21.150571 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-20 03:03:21.322303 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-20 03:03:21.512671 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-20 03:03:21.73665 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-20 03:03:21.96082 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-20 03:03:22.094667 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-20 03:03:22.225127 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-20 03:03:22.368222 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-20 03:03:22.555045 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-20 03:03:22.746963 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-20 03:03:22.916327 WARNING::Fitting problem for feature 13 a warning was issued
2024-12-20 03:03:23.07327 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-20 03:03:23.209762 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-20 03:03:23.597215 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-20 03:03:23.72695 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-20 03:03:23.909347 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-20 03:03:24.07788 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-20 03:03:24.288749 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-20 03:03:24.50268 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-20 03:03:24.72233 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-20 03:03:24.932363 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-20 03:03:25.070115 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-20 03:03:25.262537 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-20 03:03:25.428362 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-20 03:03:25.597436 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-20 03:03:25.814777 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-20 03:03:26.029954 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-20 03:03:26.233883 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-20 03:03:26.441062 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-20 03:03:26.652289 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-20 03:03:26.831753 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-20 03:03:27.019223 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-20 03:03:27.226182 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-20 03:03:27.39729 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-20 03:03:27.559695 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-20 03:03:27.700926 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-20 03:03:27.882414 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-20 03:03:28.076066 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-20 03:03:28.241343 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-20 03:03:28.378753 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-20 03:03:28.530976 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-20 03:03:28.708556 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-20 03:03:28.867223 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-20 03:03:29.066006 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-20 03:03:29.277349 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-20 03:03:29.443369 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-20 03:03:29.622131 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-20 03:03:29.82439 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-20 03:03:29.980491 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-20 03:03:30.151442 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-20 03:03:30.337207 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-20 03:03:30.529378 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-20 03:03:30.704263 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-20 03:03:30.912632 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-20 03:03:31.083164 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-20 03:03:31.282277 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-20 03:03:31.496627 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-20 03:03:31.726384 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-20 03:03:31.924758 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-20 03:03:32.135364 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-20 03:03:32.351418 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-20 03:03:32.556577 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-20 03:03:32.728812 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-20 03:03:32.911955 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-20 03:03:33.085249 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-20 03:03:33.259501 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-20 03:03:33.466836 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-20 03:03:33.673385 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-20 03:03:33.878604 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-20 03:03:34.066861 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-20 03:03:34.249822 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-20 03:03:34.754812 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-20 03:03:34.944524 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-20 03:03:35.148987 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-20 03:03:35.380535 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-20 03:03:35.519111 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-20 03:03:35.737257 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-20 03:03:35.98536 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-20 03:03:36.195627 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-20 03:03:36.409842 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-20 03:03:36.551837 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-20 03:03:36.704706 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-20 03:03:36.911706 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-20 03:03:37.131823 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-20 03:03:37.317613 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-20 03:03:37.565847 INFO::Counting total values for each feature
2024-12-20 03:03:37.624559 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-12-20 03:03:37.992362 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-12-20 03:03:38.466843 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-12-20 03:03:38.935379 INFO::Writing residuals to file output/fits/residuals.rds
2024-12-20 03:03:38.982124 INFO::Writing fitted values to file output/fits/fitted.rds
2024-12-20 03:03:39.005882 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-12-20 03:03:39.012155 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-12-20 03:03:39.036264 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"
2024-12-20 03:03:39.087836 INFO::Writing function arguments to log file
2024-12-20 03:03:39.110057 INFO::Verifying options selected are valid
2024-12-20 03:03:39.11182 INFO::Determining format of input files
2024-12-20 03:03:39.114508 INFO::Input format is data samples as rows and metadata samples as rows
2024-12-20 03:03:39.12209 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-12-20 03:03:39.124063 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-12-20 03:03:39.126541 INFO::Filter data based on min abundance and min prevalence
2024-12-20 03:03:39.128153 INFO::Total samples in data: 1595
2024-12-20 03:03:39.129707 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-12-20 03:03:39.136396 INFO::Total filtered features: 0
2024-12-20 03:03:39.139382 INFO::Filtered feature names from abundance and prevalence filtering:
2024-12-20 03:03:39.152454 INFO::Total filtered features with variance filtering: 0
2024-12-20 03:03:39.154599 INFO::Filtered feature names from variance filtering:
2024-12-20 03:03:39.156583 INFO::Running selected normalization method: NONE
2024-12-20 03:03:39.158452 INFO::Bypass z-score application to metadata
2024-12-20 03:03:39.160472 INFO::Running selected transform method: AST
2024-12-20 03:03:39.182538 INFO::Running selected analysis method: LM
2024-12-20 03:03:39.184987 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-12-20 03:03:39.351817 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-12-20 03:03:39.569652 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-12-20 03:03:39.743323 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-12-20 03:03:39.923454 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-12-20 03:03:40.105573 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-12-20 03:03:40.32582 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-12-20 03:03:40.531963 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-12-20 03:03:40.724437 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-12-20 03:03:40.878128 WARNING::Fitting problem for feature 9 a warning was issued
2024-12-20 03:03:41.020945 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-12-20 03:03:41.176402 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-12-20 03:03:41.358239 WARNING::Fitting problem for feature 11 a warning was issued
2024-12-20 03:03:41.52185 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-12-20 03:03:41.650119 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-12-20 03:03:41.800352 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-12-20 03:03:41.951546 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-12-20 03:03:42.153628 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-12-20 03:03:42.32779 WARNING::Fitting problem for feature 16 a warning was issued
2024-12-20 03:03:42.530507 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-12-20 03:03:42.716529 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-12-20 03:03:42.887489 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-12-20 03:03:43.048112 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-12-20 03:03:43.454483 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-12-20 03:03:43.592203 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-12-20 03:03:43.79324 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-12-20 03:03:43.988221 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-12-20 03:03:44.184712 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-12-20 03:03:44.381699 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-12-20 03:03:44.562479 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-12-20 03:03:44.707865 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-12-20 03:03:44.890441 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-12-20 03:03:45.060919 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-12-20 03:03:45.24575 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-12-20 03:03:45.447172 INFO::Fitting model to feature number 32, Prevotella.copri
2024-12-20 03:03:45.574624 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-12-20 03:03:45.691874 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-12-20 03:03:45.871529 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-12-20 03:03:46.024748 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-12-20 03:03:46.160395 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-12-20 03:03:46.360757 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-12-20 03:03:46.570833 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-12-20 03:03:46.705031 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-12-20 03:03:46.901099 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-12-20 03:03:47.029522 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-12-20 03:03:47.23448 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-12-20 03:03:47.397813 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-12-20 03:03:47.572713 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-12-20 03:03:47.710871 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-12-20 03:03:47.881762 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-12-20 03:03:48.0818 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-12-20 03:03:48.22433 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-12-20 03:03:48.375658 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-12-20 03:03:48.519819 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-12-20 03:03:48.714721 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-12-20 03:03:48.929647 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-12-20 03:03:49.109926 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-12-20 03:03:49.26359 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-12-20 03:03:49.44901 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-12-20 03:03:49.604648 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-12-20 03:03:49.777037 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-12-20 03:03:49.951048 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-12-20 03:03:50.1631 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-12-20 03:03:50.297115 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-12-20 03:03:50.42269 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-12-20 03:03:50.882604 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-12-20 03:03:51.064957 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-12-20 03:03:51.214408 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-12-20 03:03:51.366386 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-12-20 03:03:51.51898 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-12-20 03:03:51.714321 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-12-20 03:03:51.884415 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-12-20 03:03:52.061372 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-12-20 03:03:52.199201 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-12-20 03:03:52.326822 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-12-20 03:03:52.369496 WARNING::Fitting problem for feature 72 a warning was issued
2024-12-20 03:03:52.499447 INFO::Fitting model to feature number 73, Dialister.invisus
2024-12-20 03:03:52.676519 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-12-20 03:03:52.894403 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-12-20 03:03:53.095642 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-12-20 03:03:53.299277 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-12-20 03:03:53.500699 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-12-20 03:03:53.716482 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-12-20 03:03:53.927517 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-12-20 03:03:54.085403 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-12-20 03:03:54.305586 INFO::Fitting model to feature number 82, Escherichia.coli
2024-12-20 03:03:54.505269 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-12-20 03:03:54.65422 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-12-20 03:03:54.822034 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-12-20 03:03:54.97966 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-12-20 03:03:55.198622 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-12-20 03:03:55.39335 INFO::Counting total values for each feature
2024-12-20 03:03:55.416618 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-12-20 03:03:55.886236 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-12-20 03:03:56.190303 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-12-20 03:03:56.653502 INFO::Writing residuals to file output2/fits/residuals.rds
2024-12-20 03:03:56.725527 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-12-20 03:03:56.781331 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-12-20 03:03:56.790259 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-12-20 03:03:56.808914 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 
  39.37    0.95   41.28

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	110.03	7.58	118.16