Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-03-19 11:42 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
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" 4459
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: 2025-03-18 13:40 -0400 (Tue, 18 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 palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-03-19 03:01:28 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 03:05:12 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 224.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 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 '1.21.0'
* 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 119.5   7.89  127.66
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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"
2025-03-19 03:04:19.440534 INFO::Writing function arguments to log file
2025-03-19 03:04:19.496698 INFO::Verifying options selected are valid
2025-03-19 03:04:19.555412 INFO::Determining format of input files
2025-03-19 03:04:19.559522 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-19 03:04:19.584027 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-19 03:04:19.587783 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-19 03:04:19.593179 INFO::Filter data based on min abundance and min prevalence
2025-03-19 03:04:19.596112 INFO::Total samples in data: 1595
2025-03-19 03:04:19.598974 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-19 03:04:19.606717 INFO::Total filtered features: 0
2025-03-19 03:04:19.610402 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-19 03:04:19.625441 INFO::Total filtered features with variance filtering: 0
2025-03-19 03:04:19.628778 INFO::Filtered feature names from variance filtering:
2025-03-19 03:04:19.631762 INFO::Running selected normalization method: TSS
2025-03-19 03:04:21.114349 INFO::Bypass z-score application to metadata
2025-03-19 03:04:21.118001 INFO::Running selected transform method: AST
2025-03-19 03:04:21.145379 INFO::Running selected analysis method: LM
2025-03-19 03:04:21.796737 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-19 03:04:22.318573 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-19 03:04:22.854923 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-19 03:04:23.076 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-19 03:04:23.302632 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-19 03:04:23.587702 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-19 03:04:23.797221 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-19 03:04:23.972853 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-19 03:04:24.182742 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-19 03:04:24.402466 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-19 03:04:24.632734 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-19 03:04:24.864328 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-19 03:04:25.067857 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-19 03:04:25.26665 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-19 03:04:25.497039 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-19 03:04:25.714316 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-19 03:04:25.955686 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-19 03:04:26.176624 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-19 03:04:26.350538 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-19 03:04:26.588997 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-19 03:04:26.820933 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-19 03:04:27.014828 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-19 03:04:27.269545 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-19 03:04:27.49776 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-19 03:04:27.687358 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-19 03:04:27.892297 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-19 03:04:28.121962 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-19 03:04:28.323621 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-19 03:04:28.502342 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-19 03:04:28.730582 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-19 03:04:28.96138 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-19 03:04:29.120737 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-19 03:04:29.334227 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-19 03:04:29.517986 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-19 03:04:29.712369 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-19 03:04:29.940147 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-19 03:04:30.080153 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-19 03:04:30.266245 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-19 03:04:30.472164 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-19 03:04:30.692614 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-19 03:04:30.91473 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-19 03:04:31.14141 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-19 03:04:31.333267 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-19 03:04:31.589592 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-19 03:04:31.80416 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-19 03:04:32.018722 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-19 03:04:32.503865 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-19 03:04:32.720696 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-19 03:04:32.901464 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-19 03:04:33.151579 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-19 03:04:33.365196 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-19 03:04:33.528621 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-19 03:04:33.752809 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-19 03:04:33.931926 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-19 03:04:34.149595 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-19 03:04:34.382366 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-19 03:04:34.633152 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-19 03:04:34.875386 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-19 03:04:35.091447 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-19 03:04:35.338532 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-19 03:04:35.545252 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-19 03:04:35.756575 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-19 03:04:35.984033 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-19 03:04:36.159487 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-19 03:04:36.392099 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-19 03:04:36.61428 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-19 03:04:36.766856 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-19 03:04:36.986821 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-19 03:04:37.167183 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-19 03:04:37.330038 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-19 03:04:37.55396 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-19 03:04:37.754624 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-19 03:04:37.973731 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-19 03:04:38.218061 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-19 03:04:38.42934 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-19 03:04:38.669693 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-19 03:04:38.892879 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-19 03:04:39.126065 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-19 03:04:39.377584 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-19 03:04:39.597504 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-19 03:04:39.797206 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-19 03:04:39.960545 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-19 03:04:40.460004 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-19 03:04:40.663706 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-19 03:04:40.872676 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-19 03:04:41.092442 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-19 03:04:41.333082 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-19 03:04:41.53044 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-19 03:04:41.776649 INFO::Counting total values for each feature
2025-03-19 03:04:41.825069 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-19 03:04:42.275952 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-19 03:04:42.822017 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-19 03:04:43.238602 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-19 03:04:43.293923 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-19 03:04:43.327836 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-19 03:04:43.337433 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-19 03:04:43.363326 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"
2025-03-19 03:04:43.42303 INFO::Writing function arguments to log file
2025-03-19 03:04:43.441404 INFO::Verifying options selected are valid
2025-03-19 03:04:43.44464 INFO::Determining format of input files
2025-03-19 03:04:43.448056 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-19 03:04:43.460373 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-19 03:04:43.46364 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-19 03:04:43.467721 INFO::Filter data based on min abundance and min prevalence
2025-03-19 03:04:43.470545 INFO::Total samples in data: 1595
2025-03-19 03:04:43.473267 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-19 03:04:43.48154 INFO::Total filtered features: 0
2025-03-19 03:04:43.484711 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-19 03:04:43.49486 INFO::Total filtered features with variance filtering: 0
2025-03-19 03:04:43.497001 INFO::Filtered feature names from variance filtering:
2025-03-19 03:04:43.498753 INFO::Running selected normalization method: NONE
2025-03-19 03:04:43.500382 INFO::Bypass z-score application to metadata
2025-03-19 03:04:43.502242 INFO::Running selected transform method: AST
2025-03-19 03:04:43.521538 INFO::Running selected analysis method: LM
2025-03-19 03:04:43.524214 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-19 03:04:43.72918 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-19 03:04:43.916369 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-19 03:04:44.126608 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-19 03:04:44.337601 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-19 03:04:44.542154 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-19 03:04:44.777471 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-19 03:04:44.97702 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-19 03:04:45.16615 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-19 03:04:45.28322 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-19 03:04:45.492154 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-19 03:04:45.678625 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-19 03:04:45.837141 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-19 03:04:46.059942 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-19 03:04:46.230167 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-19 03:04:46.415122 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-19 03:04:46.62819 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-19 03:04:46.769755 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-19 03:04:46.954505 WARNING::Fitting problem for feature 16 a warning was issued
2025-03-19 03:04:47.150934 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-19 03:04:47.349193 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-19 03:04:47.517505 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-19 03:04:47.697514 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-19 03:04:47.905465 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-19 03:04:48.085408 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-19 03:04:48.288002 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-19 03:04:48.47429 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-19 03:04:48.695586 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-19 03:04:48.908716 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-19 03:04:49.13373 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-19 03:04:49.314929 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-19 03:04:49.492746 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-19 03:04:49.704363 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-19 03:04:49.916398 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-19 03:04:50.128158 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-19 03:04:50.276261 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-19 03:04:50.43271 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-19 03:04:50.641418 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-19 03:04:50.858116 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-19 03:04:51.040431 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-19 03:04:51.210644 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-19 03:04:51.414738 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-19 03:04:51.571025 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-19 03:04:51.767613 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-19 03:04:51.992872 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-19 03:04:52.194683 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-19 03:04:52.365062 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-19 03:04:52.588679 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-19 03:04:52.799267 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-19 03:04:53.018648 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-19 03:04:53.234942 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-19 03:04:53.457786 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-19 03:04:53.654389 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-19 03:04:53.822508 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-19 03:04:53.983346 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-19 03:04:54.164399 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-19 03:04:54.303884 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-19 03:04:54.487914 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-19 03:04:54.684337 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-19 03:04:54.93523 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-19 03:04:55.149867 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-19 03:04:55.366907 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-19 03:04:55.593722 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-19 03:04:55.813402 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-19 03:04:56.021927 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-19 03:04:56.217699 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-19 03:04:56.375301 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-19 03:04:56.571985 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-19 03:04:56.739781 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-19 03:04:56.928516 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-19 03:04:57.129314 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-19 03:04:57.344918 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-19 03:04:57.561454 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-19 03:04:57.767825 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-19 03:04:57.97838 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-19 03:04:58.05856 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-19 03:04:58.291555 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-19 03:04:58.505038 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-19 03:04:58.690551 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-19 03:04:58.912214 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-19 03:04:59.143513 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-19 03:04:59.30312 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-19 03:04:59.456525 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-19 03:04:59.680194 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-19 03:04:59.883016 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-19 03:05:00.042511 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-19 03:05:00.260065 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-19 03:05:00.482441 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-19 03:05:00.683476 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-19 03:05:00.878134 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-19 03:05:01.047951 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-19 03:05:01.26032 INFO::Counting total values for each feature
2025-03-19 03:05:01.292016 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-19 03:05:01.797443 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-19 03:05:02.248595 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-19 03:05:02.80804 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-19 03:05:02.892394 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-19 03:05:02.972103 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-19 03:05:02.981603 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-19 03:05:02.999815 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 
  43.85    1.50   45.50

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2119.50 7.89127.66