Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-21 11:42 -0500 (Tue, 21 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4502
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4467
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4422
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4406
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 1128/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-20 13:40 -0500 (Mon, 20 Jan 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 -0500 (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 22.03 LTS-SP1) / 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: 2025-01-21 02:37:56 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 02:41:17 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 200.7 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) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 108.5   6.56  115.39
* 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' ...
** 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 1.9.15
Current TMB package version is 1.9.16
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) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
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"
2025-01-21 02:40:32.728898 INFO::Writing function arguments to log file
2025-01-21 02:40:32.779201 INFO::Verifying options selected are valid
2025-01-21 02:40:32.811894 INFO::Determining format of input files
2025-01-21 02:40:32.814321 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 02:40:32.821564 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 02:40:32.823628 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-21 02:40:32.826804 INFO::Filter data based on min abundance and min prevalence
2025-01-21 02:40:32.828486 INFO::Total samples in data: 1595
2025-01-21 02:40:32.830146 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 02:40:32.84212 INFO::Total filtered features: 0
2025-01-21 02:40:32.844022 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 02:40:32.85227 INFO::Total filtered features with variance filtering: 0
2025-01-21 02:40:32.854273 INFO::Filtered feature names from variance filtering:
2025-01-21 02:40:32.856023 INFO::Running selected normalization method: TSS
2025-01-21 02:40:33.997571 INFO::Bypass z-score application to metadata
2025-01-21 02:40:34.000678 INFO::Running selected transform method: AST
2025-01-21 02:40:34.024057 INFO::Running selected analysis method: LM
2025-01-21 02:40:34.651247 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 02:40:35.086726 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 02:40:35.240407 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 02:40:35.390992 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 02:40:35.632611 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 02:40:35.768492 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 02:40:35.9594 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 02:40:36.203923 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 02:40:36.410731 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 02:40:36.591336 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 02:40:36.73402 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 02:40:36.888787 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 02:40:37.054055 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 02:40:37.193423 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-21 02:40:37.363526 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 02:40:37.502856 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 02:40:37.651123 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 02:40:37.82746 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 02:40:37.970715 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 02:40:38.128493 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 02:40:38.326452 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 02:40:38.546698 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 02:40:38.735189 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 02:40:38.905486 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 02:40:39.118952 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 02:40:39.32878 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 02:40:39.528747 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 02:40:39.749061 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 02:40:39.957305 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 02:40:40.089787 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 02:40:40.28344 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 02:40:40.436501 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 02:40:40.652883 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 02:40:40.867668 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 02:40:41.097855 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 02:40:41.269913 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 02:40:41.427141 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 02:40:41.886596 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 02:40:42.10068 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 02:40:42.307574 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 02:40:42.49289 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 02:40:42.654076 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 02:40:42.786581 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 02:40:42.945244 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 02:40:43.144506 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 02:40:43.342647 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 02:40:43.549051 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 02:40:43.766986 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 02:40:43.98554 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 02:40:44.131803 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 02:40:44.333669 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 02:40:44.524411 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 02:40:44.711419 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 02:40:44.911508 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 02:40:45.10645 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 02:40:45.287857 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 02:40:45.503424 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 02:40:45.653018 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 02:40:45.821348 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 02:40:46.028469 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 02:40:46.22722 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 02:40:46.380113 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 02:40:46.591606 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 02:40:46.76215 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 02:40:46.927219 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 02:40:47.063404 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 02:40:47.208459 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 02:40:47.356696 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 02:40:47.474255 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 02:40:47.606637 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 02:40:47.778608 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 02:40:47.99008 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 02:40:48.173239 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 02:40:48.349951 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 02:40:48.555044 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 02:40:48.760138 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 02:40:48.914541 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 02:40:49.062655 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 02:40:49.209032 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 02:40:49.369274 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 02:40:49.562892 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 02:40:49.71015 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 02:40:49.91742 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 02:40:50.110815 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 02:40:50.309008 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 02:40:50.510166 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 02:40:50.728604 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 02:40:50.865436 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 02:40:51.060134 INFO::Counting total values for each feature
2025-01-21 02:40:51.11884 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-21 02:40:51.580338 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-21 02:40:52.022277 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-21 02:40:52.414311 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-21 02:40:52.45738 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-21 02:40:52.480819 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-21 02:40:52.486924 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-21 02:40:52.501992 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"
2025-01-21 02:40:52.560812 INFO::Writing function arguments to log file
2025-01-21 02:40:52.579953 INFO::Verifying options selected are valid
2025-01-21 02:40:52.582596 INFO::Determining format of input files
2025-01-21 02:40:52.585485 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-21 02:40:52.59263 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-21 02:40:52.594472 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-21 02:40:52.5968 INFO::Filter data based on min abundance and min prevalence
2025-01-21 02:40:52.598372 INFO::Total samples in data: 1595
2025-01-21 02:40:52.599901 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-21 02:40:52.605054 INFO::Total filtered features: 0
2025-01-21 02:40:52.606898 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-21 02:40:52.615284 INFO::Total filtered features with variance filtering: 0
2025-01-21 02:40:52.6177 INFO::Filtered feature names from variance filtering:
2025-01-21 02:40:52.6196 INFO::Running selected normalization method: NONE
2025-01-21 02:40:52.621234 INFO::Bypass z-score application to metadata
2025-01-21 02:40:52.622857 INFO::Running selected transform method: AST
2025-01-21 02:40:52.64549 INFO::Running selected analysis method: LM
2025-01-21 02:40:52.648349 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-21 02:40:52.791215 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-21 02:40:52.936104 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-21 02:40:53.078372 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-21 02:40:53.222357 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-21 02:40:53.38187 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-21 02:40:53.554752 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-21 02:40:53.690993 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-21 02:40:53.83994 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-21 02:40:54.02696 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-21 02:40:54.192661 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-21 02:40:54.358384 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-21 02:40:54.471359 WARNING::Fitting problem for feature 11 a warning was issued
2025-01-21 02:40:54.603657 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-21 02:40:54.744677 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-21 02:40:54.86875 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-21 02:40:54.991697 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-21 02:40:55.138677 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-21 02:40:55.235219 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-21 02:40:55.414019 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-21 02:40:55.586241 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-21 02:40:55.714177 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-21 02:40:55.892872 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-21 02:40:56.083407 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-21 02:40:56.224131 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-21 02:40:56.380208 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-21 02:40:56.528758 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-21 02:40:56.724387 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-21 02:40:56.870476 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-21 02:40:57.003884 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-21 02:40:57.157089 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-21 02:40:57.363565 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-21 02:40:57.556447 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-21 02:40:57.770159 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-21 02:40:57.939666 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-21 02:40:58.144431 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-21 02:40:58.285597 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-21 02:40:58.417542 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-21 02:40:58.541408 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-21 02:40:58.682612 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-21 02:40:58.813891 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-21 02:40:58.943443 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-21 02:40:59.077611 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-21 02:40:59.26575 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-21 02:40:59.416964 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-21 02:40:59.555613 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-21 02:40:59.761123 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-21 02:40:59.975468 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-21 02:41:00.133981 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-21 02:41:00.331045 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-21 02:41:00.479517 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-21 02:41:00.662698 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-21 02:41:00.815894 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-21 02:41:00.971259 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-21 02:41:01.169493 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-21 02:41:01.345897 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-21 02:41:01.503183 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-21 02:41:01.915244 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-21 02:41:02.111984 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-21 02:41:02.299219 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-21 02:41:02.447465 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-21 02:41:02.634308 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-21 02:41:02.846713 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-21 02:41:02.989695 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-21 02:41:03.116736 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-21 02:41:03.309129 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-21 02:41:03.523625 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-21 02:41:03.678061 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-21 02:41:03.874902 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-21 02:41:04.074805 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-21 02:41:04.290704 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-21 02:41:04.455603 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-21 02:41:04.625329 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-21 02:41:04.822128 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-21 02:41:05.03813 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-21 02:41:05.125269 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-21 02:41:05.261613 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-21 02:41:05.388929 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-21 02:41:05.530145 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-21 02:41:05.707846 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-21 02:41:05.906562 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-21 02:41:06.074256 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-21 02:41:06.204657 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-21 02:41:06.401888 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-21 02:41:06.591937 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-21 02:41:06.748085 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-21 02:41:06.904665 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-21 02:41:07.059894 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-21 02:41:07.273019 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-21 02:41:07.436862 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-21 02:41:07.604009 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-21 02:41:07.842794 INFO::Counting total values for each feature
2025-01-21 02:41:07.874087 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-21 02:41:08.265366 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-21 02:41:08.626026 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-21 02:41:09.122205 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-21 02:41:09.180364 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-21 02:41:09.235604 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-21 02:41:09.242021 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-21 02:41:09.253758 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 
  36.75    1.14   37.98

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2108.50 6.56115.39