Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-22 11:45 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4547
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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

Package 1141/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-03-21 20:06:51 -0400 (Fri, 21 Mar 2025)
EndedAt: 2025-03-21 20:07:48 -0400 (Fri, 21 Mar 2025)
EllapsedTime: 57.8 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) (2025-03-02 r87868)
* 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 29.765  0.581  30.476
* 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
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.16
Current TMB package version is 1.9.17
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)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-02 r87868) -- "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"
2025-03-21 20:07:35.184601 INFO::Writing function arguments to log file
2025-03-21 20:07:35.203601 INFO::Verifying options selected are valid
2025-03-21 20:07:35.217062 INFO::Determining format of input files
2025-03-21 20:07:35.217662 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 20:07:35.219754 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 20:07:35.220208 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-21 20:07:35.220999 INFO::Filter data based on min abundance and min prevalence
2025-03-21 20:07:35.221283 INFO::Total samples in data: 1595
2025-03-21 20:07:35.221569 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 20:07:35.22583 INFO::Total filtered features: 0
2025-03-21 20:07:35.226248 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 20:07:35.229249 INFO::Total filtered features with variance filtering: 0
2025-03-21 20:07:35.229583 INFO::Filtered feature names from variance filtering:
2025-03-21 20:07:35.22985 INFO::Running selected normalization method: TSS
2025-03-21 20:07:35.648001 INFO::Bypass z-score application to metadata
2025-03-21 20:07:35.648472 INFO::Running selected transform method: AST
2025-03-21 20:07:35.654354 INFO::Running selected analysis method: LM
2025-03-21 20:07:35.861157 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 20:07:35.990973 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 20:07:36.055011 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 20:07:36.111645 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 20:07:36.175188 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 20:07:36.233099 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 20:07:36.297663 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 20:07:36.35631 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 20:07:36.416611 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 20:07:36.458694 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-21 20:07:36.531686 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 20:07:36.584045 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 20:07:36.636661 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 20:07:36.692823 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 20:07:36.746464 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 20:07:36.808793 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 20:07:36.863745 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 20:07:36.918847 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 20:07:36.973744 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 20:07:37.032383 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 20:07:37.084594 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 20:07:37.144177 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 20:07:37.197304 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 20:07:37.252551 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 20:07:37.305545 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 20:07:37.358573 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 20:07:37.41621 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 20:07:37.472296 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 20:07:37.527695 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 20:07:37.584059 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 20:07:37.641979 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 20:07:37.696727 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 20:07:37.75258 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 20:07:37.809016 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 20:07:37.867294 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 20:07:37.932046 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 20:07:37.984872 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 20:07:38.044027 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 20:07:38.099333 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 20:07:38.154733 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 20:07:38.208235 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 20:07:38.271204 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 20:07:38.326278 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 20:07:38.387874 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 20:07:38.437512 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 20:07:38.48977 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 20:07:38.545172 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 20:07:38.597099 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 20:07:38.750173 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 20:07:38.802517 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 20:07:38.857091 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 20:07:38.915493 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 20:07:38.967935 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 20:07:39.020086 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 20:07:39.080361 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 20:07:39.128994 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 20:07:39.18218 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 20:07:39.241972 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 20:07:39.290872 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 20:07:39.344287 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 20:07:39.398309 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 20:07:39.448872 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 20:07:39.501032 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 20:07:39.558376 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 20:07:39.608103 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 20:07:39.654689 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 20:07:39.707156 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 20:07:39.757747 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 20:07:39.814049 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 20:07:39.864165 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 20:07:39.917541 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 20:07:39.970312 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 20:07:40.018276 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 20:07:40.072231 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 20:07:40.122255 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 20:07:40.173126 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 20:07:40.225377 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 20:07:40.273059 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 20:07:40.330627 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 20:07:40.382908 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 20:07:40.439175 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 20:07:40.489369 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 20:07:40.545695 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 20:07:40.597895 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 20:07:40.651429 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 20:07:40.705705 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 20:07:40.758403 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 20:07:40.81178 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 20:07:40.876439 INFO::Counting total values for each feature
2025-03-21 20:07:40.891644 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-21 20:07:40.938911 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-21 20:07:40.994039 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-21 20:07:41.048786 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-21 20:07:41.07566 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-21 20:07:41.09072 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-21 20:07:41.093722 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-21 20:07:41.096574 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"
2025-03-21 20:07:41.101491 INFO::Writing function arguments to log file
2025-03-21 20:07:41.103378 INFO::Verifying options selected are valid
2025-03-21 20:07:41.103672 INFO::Determining format of input files
2025-03-21 20:07:41.104093 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-21 20:07:41.10924 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-21 20:07:41.109676 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-21 20:07:41.110215 INFO::Filter data based on min abundance and min prevalence
2025-03-21 20:07:41.110498 INFO::Total samples in data: 1595
2025-03-21 20:07:41.11077 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-21 20:07:41.112287 INFO::Total filtered features: 0
2025-03-21 20:07:41.112631 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-21 20:07:41.115367 INFO::Total filtered features with variance filtering: 0
2025-03-21 20:07:41.115733 INFO::Filtered feature names from variance filtering:
2025-03-21 20:07:41.116011 INFO::Running selected normalization method: NONE
2025-03-21 20:07:41.116275 INFO::Bypass z-score application to metadata
2025-03-21 20:07:41.116534 INFO::Running selected transform method: AST
2025-03-21 20:07:41.134982 INFO::Running selected analysis method: LM
2025-03-21 20:07:41.13585 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-21 20:07:41.186788 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-21 20:07:41.238265 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-21 20:07:41.290294 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-21 20:07:41.341834 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-21 20:07:41.397891 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-21 20:07:41.450503 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-21 20:07:41.505325 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-21 20:07:41.553866 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-21 20:07:41.603468 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-21 20:07:41.660166 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-21 20:07:41.702498 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-21 20:07:41.759749 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-21 20:07:41.816195 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-21 20:07:41.858985 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-21 20:07:41.913343 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-21 20:07:41.968802 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-21 20:07:42.021013 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-21 20:07:42.072346 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-21 20:07:42.128504 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-21 20:07:42.179174 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-21 20:07:42.232015 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-21 20:07:42.281845 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-21 20:07:42.333647 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-21 20:07:42.387636 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-21 20:07:42.435214 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-21 20:07:42.491143 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-21 20:07:42.540839 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-21 20:07:42.595765 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-21 20:07:42.647206 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-21 20:07:42.699594 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-21 20:07:42.747157 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-21 20:07:42.802271 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-21 20:07:42.852377 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-21 20:07:42.908917 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-21 20:07:42.956864 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-21 20:07:43.013431 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-21 20:07:43.064264 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-21 20:07:43.118196 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-21 20:07:43.171446 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-21 20:07:43.221256 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-21 20:07:43.27742 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-21 20:07:43.325743 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-21 20:07:43.382535 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-21 20:07:43.431239 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-21 20:07:43.483423 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-21 20:07:43.54057 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-21 20:07:43.590465 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-21 20:07:43.645061 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-21 20:07:43.698923 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-21 20:07:43.750506 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-21 20:07:43.80602 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-21 20:07:43.853926 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-21 20:07:43.908171 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-21 20:07:43.960523 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-21 20:07:44.006976 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-21 20:07:44.058948 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-21 20:07:44.106972 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-21 20:07:44.165252 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-21 20:07:44.214628 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-21 20:07:44.266196 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-21 20:07:44.327141 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-21 20:07:44.378524 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-21 20:07:44.433911 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-21 20:07:44.482656 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-21 20:07:44.533729 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-21 20:07:44.590414 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-21 20:07:44.64209 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-21 20:07:44.698793 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-21 20:07:44.752125 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-21 20:07:44.80588 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-21 20:07:44.858329 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-21 20:07:44.911658 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-21 20:07:44.965913 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-21 20:07:44.984037 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-21 20:07:45.043111 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-21 20:07:45.096173 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-21 20:07:45.156448 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-21 20:07:45.210244 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-21 20:07:45.266032 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-21 20:07:45.316583 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-21 20:07:45.374808 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-21 20:07:45.433236 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-21 20:07:45.483295 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-21 20:07:45.551076 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-21 20:07:45.603256 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-21 20:07:45.662044 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-21 20:07:45.709903 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-21 20:07:45.759606 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-21 20:07:45.819053 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-21 20:07:45.879405 INFO::Counting total values for each feature
2025-03-21 20:07:45.893481 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-21 20:07:45.942764 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-21 20:07:45.990453 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-21 20:07:46.046144 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-21 20:07:46.083028 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-21 20:07:46.118204 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-21 20:07:46.121365 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-21 20:07:46.123773 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 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 11.068   0.312  11.391 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin229.765 0.58130.476