Multiple platform build/check report for BioC 3.21 - CHECK results for Maaslin2 on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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 kjohnson3

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: 1.21.0

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_1.21.0.tar.gz

StartedAt: 2025-02-05 19:59:16 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 20:00:14 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 58.7 seconds

RetCode: 0

Status: OK

CheckDir: Maaslin2.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 29.593  0.561  30.316
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.21.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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"
2025-02-05 20:00:00.002539 INFO::Writing function arguments to log file
2025-02-05 20:00:00.020434 INFO::Verifying options selected are valid
2025-02-05 20:00:00.033972 INFO::Determining format of input files
2025-02-05 20:00:00.034614 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 20:00:00.036983 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-05 20:00:00.037476 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-05 20:00:00.038341 INFO::Filter data based on min abundance and min prevalence
2025-02-05 20:00:00.03865 INFO::Total samples in data: 1595
2025-02-05 20:00:00.038931 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-05 20:00:00.043383 INFO::Total filtered features: 0
2025-02-05 20:00:00.043863 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 20:00:00.047111 INFO::Total filtered features with variance filtering: 0
2025-02-05 20:00:00.047521 INFO::Filtered feature names from variance filtering:
2025-02-05 20:00:00.047851 INFO::Running selected normalization method: TSS
2025-02-05 20:00:00.463866 INFO::Bypass z-score application to metadata
2025-02-05 20:00:00.464355 INFO::Running selected transform method: AST
2025-02-05 20:00:00.470109 INFO::Running selected analysis method: LM
2025-02-05 20:00:00.670132 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-05 20:00:00.798835 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-05 20:00:00.861671 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-05 20:00:00.915732 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-05 20:00:00.974204 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-05 20:00:01.02938 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-05 20:00:01.086345 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-05 20:00:01.13789 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-05 20:00:01.192605 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-05 20:00:01.242686 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-05 20:00:01.311895 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-05 20:00:01.363403 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-05 20:00:01.413916 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-05 20:00:01.473677 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-05 20:00:01.518101 WARNING::Fitting problem for feature 14 a warning was issued
2025-02-05 20:00:01.580156 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-05 20:00:01.636588 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-05 20:00:01.695781 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-05 20:00:01.752 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-05 20:00:01.811851 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-05 20:00:01.865736 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-05 20:00:01.921369 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-05 20:00:01.974781 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-05 20:00:02.030079 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-05 20:00:02.079116 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-05 20:00:02.133104 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-05 20:00:02.189825 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-05 20:00:02.239851 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-05 20:00:02.300981 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-05 20:00:02.359503 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-05 20:00:02.420243 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-05 20:00:02.474499 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-05 20:00:02.541831 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-05 20:00:02.595192 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-05 20:00:02.656896 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-05 20:00:02.708277 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-05 20:00:02.766016 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-05 20:00:02.821302 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-05 20:00:02.881168 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-05 20:00:02.931144 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-05 20:00:02.986602 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-05 20:00:03.041304 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-05 20:00:03.09829 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-05 20:00:03.152607 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-05 20:00:03.209687 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-05 20:00:03.261495 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-05 20:00:03.311835 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-05 20:00:03.368035 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-05 20:00:03.425954 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-05 20:00:03.476371 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-05 20:00:03.635851 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-05 20:00:03.686507 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-05 20:00:03.740626 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-05 20:00:03.800621 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-05 20:00:03.856706 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-05 20:00:03.909758 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-05 20:00:03.972359 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-05 20:00:04.027552 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-05 20:00:04.07654 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-05 20:00:04.136341 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-05 20:00:04.187696 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-05 20:00:04.239678 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-05 20:00:04.29506 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-05 20:00:04.346699 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-05 20:00:04.398585 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-05 20:00:04.452404 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-05 20:00:04.50177 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-05 20:00:04.552455 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-05 20:00:04.594447 WARNING::Fitting problem for feature 67 a warning was issued
2025-02-05 20:00:04.645504 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-05 20:00:04.697045 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-05 20:00:04.75529 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-05 20:00:04.809717 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-05 20:00:04.869607 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-05 20:00:04.919136 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-05 20:00:04.970158 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-05 20:00:05.031354 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-05 20:00:05.084202 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-05 20:00:05.137433 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-05 20:00:05.196204 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-05 20:00:05.250392 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-05 20:00:05.304176 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-05 20:00:05.359952 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-05 20:00:05.412471 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-05 20:00:05.464871 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-05 20:00:05.517602 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-05 20:00:05.567627 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-05 20:00:05.619447 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-05 20:00:05.676018 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-05 20:00:05.744439 INFO::Counting total values for each feature
2025-02-05 20:00:05.762878 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-05 20:00:05.810952 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-05 20:00:05.867318 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-05 20:00:05.928643 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-05 20:00:05.956009 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-05 20:00:05.970931 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-05 20:00:05.974197 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-05 20:00:05.977128 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"
2025-02-05 20:00:05.982497 INFO::Writing function arguments to log file
2025-02-05 20:00:05.98474 INFO::Verifying options selected are valid
2025-02-05 20:00:05.985097 INFO::Determining format of input files
2025-02-05 20:00:05.985531 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-05 20:00:05.987587 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-05 20:00:05.987976 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-05 20:00:05.988543 INFO::Filter data based on min abundance and min prevalence
2025-02-05 20:00:05.988833 INFO::Total samples in data: 1595
2025-02-05 20:00:05.989112 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-05 20:00:05.990714 INFO::Total filtered features: 0
2025-02-05 20:00:05.991032 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-05 20:00:05.99373 INFO::Total filtered features with variance filtering: 0
2025-02-05 20:00:05.994071 INFO::Filtered feature names from variance filtering:
2025-02-05 20:00:05.994347 INFO::Running selected normalization method: NONE
2025-02-05 20:00:05.994609 INFO::Bypass z-score application to metadata
2025-02-05 20:00:05.99487 INFO::Running selected transform method: AST
2025-02-05 20:00:06.003743 INFO::Running selected analysis method: LM
2025-02-05 20:00:06.004408 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-05 20:00:06.054582 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-05 20:00:06.107608 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-05 20:00:06.16342 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-05 20:00:06.212798 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-05 20:00:06.261527 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-05 20:00:06.325948 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-05 20:00:06.375197 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-05 20:00:06.424362 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-05 20:00:06.47903 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-05 20:00:06.529118 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-05 20:00:06.581292 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-05 20:00:06.635778 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-05 20:00:06.684529 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-05 20:00:06.734614 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-05 20:00:06.791879 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-05 20:00:06.831694 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-05 20:00:06.887566 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-05 20:00:06.939727 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-05 20:00:06.991648 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-05 20:00:07.03864 WARNING::Fitting problem for feature 19 a warning was issued
2025-02-05 20:00:07.087928 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-05 20:00:07.140743 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-05 20:00:07.195934 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-05 20:00:07.2465 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-05 20:00:07.293879 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-05 20:00:07.347515 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-05 20:00:07.396501 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-05 20:00:07.54554 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-05 20:00:07.596192 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-05 20:00:07.64508 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-05 20:00:07.695292 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-05 20:00:07.749508 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-05 20:00:07.798472 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-05 20:00:07.849599 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-05 20:00:07.899009 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-05 20:00:07.953483 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-05 20:00:08.002489 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-05 20:00:08.054618 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-05 20:00:08.108588 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-05 20:00:08.157608 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-05 20:00:08.205209 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-05 20:00:08.255022 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-05 20:00:08.309341 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-05 20:00:08.359677 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-05 20:00:08.413206 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-05 20:00:08.468702 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-05 20:00:08.519674 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-05 20:00:08.571611 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-05 20:00:08.624838 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-05 20:00:08.6758 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-05 20:00:08.725572 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-05 20:00:08.777104 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-05 20:00:08.829547 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-05 20:00:08.875448 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-05 20:00:08.925772 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-05 20:00:08.972021 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-05 20:00:09.020061 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-05 20:00:09.076976 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-05 20:00:09.124774 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-05 20:00:09.172883 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-05 20:00:09.226616 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-05 20:00:09.273546 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-05 20:00:09.327044 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-05 20:00:09.375135 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-05 20:00:09.423635 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-05 20:00:09.475764 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-05 20:00:09.525683 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-05 20:00:09.576392 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-05 20:00:09.626199 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-05 20:00:09.677557 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-05 20:00:09.728642 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-05 20:00:09.781107 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-05 20:00:09.835672 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-05 20:00:09.85341 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-05 20:00:09.90468 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-05 20:00:09.953691 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-05 20:00:10.008494 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-05 20:00:10.059343 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-05 20:00:10.11399 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-05 20:00:10.161596 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-05 20:00:10.226195 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-05 20:00:10.278488 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-05 20:00:10.331839 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-05 20:00:10.390671 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-05 20:00:10.440222 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-05 20:00:10.487748 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-05 20:00:10.540039 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-05 20:00:10.587894 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-05 20:00:10.638183 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-05 20:00:10.699887 INFO::Counting total values for each feature
2025-02-05 20:00:10.708261 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-05 20:00:10.755379 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-05 20:00:10.804088 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-05 20:00:10.859612 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-05 20:00:10.896149 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-05 20:00:10.931044 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-05 20:00:10.934067 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-05 20:00:10.936266 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 
 11.034   0.320  11.375

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

name	user	system	elapsed
Maaslin2	29.593	0.561	30.316