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This page was generated on 2025-03-20 12:07 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on palomino8

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

raw results


Summary

Package: Maaslin2
Version: 1.20.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-03-18 02:48:47 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 02:52:19 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 212.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

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


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Maaslin2/DESCRIPTION' ... OK
* this is package 'Maaslin2' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Maaslin2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  'xnames'
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 114.21   6.89  121.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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 version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
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"
2025-03-18 02:51:30.904137 INFO::Writing function arguments to log file
2025-03-18 02:51:30.957783 INFO::Verifying options selected are valid
2025-03-18 02:51:31.010581 INFO::Determining format of input files
2025-03-18 02:51:31.014093 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 02:51:31.025611 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 02:51:31.029112 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-18 02:51:31.034397 INFO::Filter data based on min abundance and min prevalence
2025-03-18 02:51:31.037215 INFO::Total samples in data: 1595
2025-03-18 02:51:31.050781 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 02:51:31.059281 INFO::Total filtered features: 0
2025-03-18 02:51:31.062304 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 02:51:31.076253 INFO::Total filtered features with variance filtering: 0
2025-03-18 02:51:31.079355 INFO::Filtered feature names from variance filtering:
2025-03-18 02:51:31.082093 INFO::Running selected normalization method: TSS
2025-03-18 02:51:32.635658 INFO::Bypass z-score application to metadata
2025-03-18 02:51:32.63771 INFO::Running selected transform method: AST
2025-03-18 02:51:32.655917 INFO::Running selected analysis method: LM
2025-03-18 02:51:33.108876 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 02:51:33.632331 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 02:51:33.793057 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 02:51:34.215642 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 02:51:34.409762 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 02:51:34.620243 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 02:51:34.844758 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 02:51:35.020122 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 02:51:35.218567 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 02:51:35.411119 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 02:51:35.638373 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 02:51:35.829858 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 02:51:36.018461 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 02:51:36.140984 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 02:51:36.324296 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 02:51:36.475295 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 02:51:36.632534 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 02:51:36.782844 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 02:51:36.928389 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 02:51:37.118002 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 02:51:37.321455 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 02:51:37.49859 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 02:51:37.711198 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 02:51:37.907446 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 02:51:38.093075 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 02:51:38.305731 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 02:51:38.516421 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 02:51:38.690546 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 02:51:38.852892 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 02:51:38.984104 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 02:51:39.141228 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 02:51:39.336559 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 02:51:39.55773 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 02:51:39.782571 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 02:51:39.947306 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 02:51:40.077026 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 02:51:40.252368 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 02:51:40.45975 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 02:51:40.66595 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 02:51:40.87374 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 02:51:41.071071 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 02:51:41.300016 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 02:51:41.515374 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 02:51:41.648576 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 02:51:41.800026 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 02:51:41.996411 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 02:51:42.181597 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 02:51:42.345742 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 02:51:42.517354 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 02:51:42.730813 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 02:51:42.935403 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 02:51:43.148303 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 02:51:43.35827 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 02:51:43.572428 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 02:51:43.791943 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 02:51:43.945779 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 02:51:44.076111 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 02:51:44.226776 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 02:51:44.348215 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 02:51:44.552149 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 02:51:44.755045 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 02:51:44.971313 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 02:51:45.193612 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 02:51:45.407151 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 02:51:45.614771 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 02:51:45.821927 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 02:51:46.048869 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 02:51:46.230705 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 02:51:46.390378 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 02:51:46.625802 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 02:51:46.82324 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 02:51:47.043381 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 02:51:47.272947 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 02:51:47.477531 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 02:51:47.693035 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 02:51:47.914424 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 02:51:48.078838 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 02:51:48.273663 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 02:51:48.484727 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 02:51:48.648442 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 02:51:48.803038 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 02:51:48.958017 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 02:51:49.167628 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 02:51:49.383363 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 02:51:49.60217 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 02:51:49.811569 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 02:51:50.035547 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 02:51:50.241294 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 02:51:50.531534 INFO::Counting total values for each feature
2025-03-18 02:51:50.587827 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-18 02:51:51.052072 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-18 02:51:51.410261 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-18 02:51:51.818055 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-18 02:51:51.878093 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-18 02:51:51.915249 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-18 02:51:51.924246 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-18 02:51:51.948358 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"
2025-03-18 02:51:52.08177 INFO::Writing function arguments to log file
2025-03-18 02:51:52.103108 INFO::Verifying options selected are valid
2025-03-18 02:51:52.105765 INFO::Determining format of input files
2025-03-18 02:51:52.1087 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 02:51:52.119743 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 02:51:52.122764 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-18 02:51:52.126667 INFO::Filter data based on min abundance and min prevalence
2025-03-18 02:51:52.129271 INFO::Total samples in data: 1595
2025-03-18 02:51:52.131232 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 02:51:52.152429 INFO::Total filtered features: 0
2025-03-18 02:51:52.156327 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 02:51:52.172359 INFO::Total filtered features with variance filtering: 0
2025-03-18 02:51:52.175974 INFO::Filtered feature names from variance filtering:
2025-03-18 02:51:52.178942 INFO::Running selected normalization method: NONE
2025-03-18 02:51:52.181703 INFO::Bypass z-score application to metadata
2025-03-18 02:51:52.184328 INFO::Running selected transform method: AST
2025-03-18 02:51:52.204361 INFO::Running selected analysis method: LM
2025-03-18 02:51:52.208003 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 02:51:52.411392 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 02:51:52.594615 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 02:51:52.811887 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 02:51:53.006829 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 02:51:53.19656 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 02:51:53.372263 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 02:51:53.58887 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 02:51:53.78125 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 02:51:53.951076 WARNING::Fitting problem for feature 9 a warning was issued
2025-03-18 02:51:54.476948 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 02:51:54.630476 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 02:51:54.807092 WARNING::Fitting problem for feature 11 a warning was issued
2025-03-18 02:51:54.979267 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 02:51:55.128773 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 02:51:55.290607 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 02:51:55.450358 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 02:51:55.636869 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 02:51:55.737074 WARNING::Fitting problem for feature 16 a warning was issued
2025-03-18 02:51:55.899156 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 02:51:56.026128 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 02:51:56.166014 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 02:51:56.288566 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 02:51:56.429355 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 02:51:56.553647 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 02:51:56.73102 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 02:51:56.920425 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 02:51:57.118967 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 02:51:57.295434 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 02:51:57.491951 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 02:51:57.670582 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 02:51:57.839724 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 02:51:57.972634 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 02:51:58.152386 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 02:51:58.364015 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 02:51:58.53882 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 02:51:58.698771 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 02:51:58.844988 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 02:51:58.991359 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 02:51:59.11572 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 02:51:59.276465 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 02:51:59.463878 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 02:51:59.661198 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 02:51:59.811696 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 02:51:59.960466 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 02:52:00.158997 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 02:52:00.299058 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 02:52:00.458536 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 02:52:00.655092 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 02:52:00.878416 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 02:52:01.069741 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 02:52:01.269223 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 02:52:01.453589 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 02:52:01.626493 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 02:52:01.831802 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 02:52:02.033254 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 02:52:02.243078 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 02:52:02.441402 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 02:52:02.646424 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 02:52:02.849972 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 02:52:03.042438 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 02:52:03.232399 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 02:52:03.447929 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 02:52:03.614357 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 02:52:03.788076 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 02:52:03.993838 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 02:52:04.137827 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 02:52:04.275504 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 02:52:04.416677 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 02:52:04.611783 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 02:52:04.761877 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 02:52:04.938113 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 02:52:05.139234 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 02:52:05.324454 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 02:52:05.52425 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 02:52:05.596524 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-18 02:52:05.853537 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 02:52:06.070305 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 02:52:06.278589 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 02:52:06.492239 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 02:52:06.93682 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 02:52:07.124834 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 02:52:07.269621 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 02:52:07.462681 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 02:52:07.623156 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 02:52:07.771064 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 02:52:07.947314 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 02:52:08.14842 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 02:52:08.366479 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 02:52:08.494543 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 02:52:08.651009 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 02:52:08.846639 INFO::Counting total values for each feature
2025-03-18 02:52:08.885535 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-18 02:52:09.332295 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-18 02:52:09.751276 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-18 02:52:10.180429 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-18 02:52:10.258661 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-18 02:52:10.324872 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-18 02:52:10.333707 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-18 02:52:10.353108 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 
  40.12    0.81   41.00

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2114.21 6.89121.42