Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-02-04 11:40 -0500 (Tue, 04 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4716
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4478
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4489
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4442
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 1132/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 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

CHECK results for Maaslin2 on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-02-03 23:49:37 -0500 (Mon, 03 Feb 2025)
EndedAt: 2025-02-03 23:53:53 -0500 (Mon, 03 Feb 2025)
EllapsedTime: 256.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 89.623  0.896  90.533
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-02-03 23:51:38.034769 INFO::Writing function arguments to log file
2025-02-03 23:51:38.073599 INFO::Verifying options selected are valid
2025-02-03 23:51:38.10674 INFO::Determining format of input files
2025-02-03 23:51:38.108316 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-03 23:51:38.113432 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-03 23:51:38.11471 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-03 23:51:38.117058 INFO::Filter data based on min abundance and min prevalence
2025-02-03 23:51:38.117957 INFO::Total samples in data: 1595
2025-02-03 23:51:38.118797 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-03 23:51:38.128654 INFO::Total filtered features: 0
2025-02-03 23:51:38.12979 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-03 23:51:38.136415 INFO::Total filtered features with variance filtering: 0
2025-02-03 23:51:38.137427 INFO::Filtered feature names from variance filtering:
2025-02-03 23:51:38.138304 INFO::Running selected normalization method: TSS
2025-02-03 23:51:39.339579 INFO::Bypass z-score application to metadata
2025-02-03 23:51:39.340885 INFO::Running selected transform method: AST
2025-02-03 23:51:39.356967 INFO::Running selected analysis method: LM
2025-02-03 23:51:39.897881 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-03 23:51:40.234366 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-03 23:51:40.390257 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-03 23:51:40.546615 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-03 23:51:40.713162 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-03 23:51:40.862561 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-03 23:51:41.009164 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-03 23:51:41.163958 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-03 23:51:41.279429 WARNING::Fitting problem for feature 8 a warning was issued
2025-02-03 23:51:41.456759 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-03 23:51:41.59178 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-03 23:51:41.78278 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-03 23:51:41.928563 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-03 23:51:42.072868 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-03 23:51:42.258512 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-03 23:51:42.38125 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-03 23:51:42.533022 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-03 23:51:42.680507 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-03 23:51:42.824467 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-03 23:51:42.96327 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-03 23:51:43.117071 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-03 23:51:43.2857 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-03 23:51:43.432845 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-03 23:51:43.579581 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-03 23:51:43.732002 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-03 23:51:43.876127 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-03 23:51:44.017713 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-03 23:51:44.171121 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-03 23:51:44.326952 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-03 23:51:44.472958 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-03 23:51:44.626806 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-03 23:51:44.776102 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-03 23:51:44.948607 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-03 23:51:45.120057 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-03 23:51:45.287605 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-03 23:51:45.438785 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-03 23:51:45.608604 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-03 23:51:45.758372 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-03 23:51:45.904634 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-03 23:51:46.05636 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-03 23:51:46.204028 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-03 23:51:46.351673 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-03 23:51:46.492918 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-03 23:51:46.638834 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-03 23:51:46.79038 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-03 23:51:46.938361 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-03 23:51:47.086127 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-03 23:51:47.221447 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-03 23:51:47.37345 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-03 23:51:47.522501 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-03 23:51:47.68425 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-03 23:51:47.830828 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-03 23:51:47.99421 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-03 23:51:48.134705 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-03 23:51:48.290476 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-03 23:51:48.441922 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-03 23:51:48.599113 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-03 23:51:48.749523 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-03 23:51:48.924476 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-03 23:51:49.102183 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-03 23:51:49.251919 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-03 23:51:49.413725 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-03 23:51:49.596997 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-03 23:51:49.740716 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-03 23:51:49.896716 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-03 23:51:50.061398 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-03 23:51:50.243389 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-03 23:51:50.405892 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-03 23:51:50.854069 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-03 23:51:50.994538 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-03 23:51:51.152425 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-03 23:51:51.301141 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-03 23:51:51.469738 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-03 23:51:51.625337 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-03 23:51:51.767808 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-03 23:51:51.911496 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-03 23:51:52.061357 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-03 23:51:52.201241 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-03 23:51:52.346984 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-03 23:51:52.501566 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-03 23:51:52.667452 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-03 23:51:52.846583 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-03 23:51:53.000306 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-03 23:51:53.15174 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-03 23:51:53.319487 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-03 23:51:53.491683 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-03 23:51:53.633548 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-03 23:51:53.770599 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-03 23:51:53.905575 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-03 23:51:54.052601 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-03 23:51:54.254243 INFO::Counting total values for each feature
2025-02-03 23:51:54.284463 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-03 23:51:54.380355 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-03 23:51:54.479083 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-03 23:51:54.580546 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-03 23:51:54.629488 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-03 23:51:54.657146 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-03 23:51:54.662884 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-03 23:51:54.668555 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-02-03 23:51:54.681935 INFO::Writing function arguments to log file
2025-02-03 23:51:54.68798 INFO::Verifying options selected are valid
2025-02-03 23:51:54.689052 INFO::Determining format of input files
2025-02-03 23:51:54.690331 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-03 23:51:54.695521 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-03 23:51:54.69664 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-03 23:51:54.698277 INFO::Filter data based on min abundance and min prevalence
2025-02-03 23:51:54.699236 INFO::Total samples in data: 1595
2025-02-03 23:51:54.70013 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-03 23:51:54.704408 INFO::Total filtered features: 0
2025-02-03 23:51:54.705498 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-03 23:51:54.723122 INFO::Total filtered features with variance filtering: 0
2025-02-03 23:51:54.724481 INFO::Filtered feature names from variance filtering:
2025-02-03 23:51:54.725376 INFO::Running selected normalization method: NONE
2025-02-03 23:51:54.72626 INFO::Bypass z-score application to metadata
2025-02-03 23:51:54.727104 INFO::Running selected transform method: AST
2025-02-03 23:51:54.740602 INFO::Running selected analysis method: LM
2025-02-03 23:51:54.74213 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-03 23:51:54.883287 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-03 23:51:55.023086 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-03 23:51:55.159839 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-03 23:51:55.297446 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-03 23:51:55.429277 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-03 23:51:55.573621 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-03 23:51:55.726834 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-03 23:51:55.869373 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-03 23:51:56.012836 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-03 23:51:56.159486 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-03 23:51:56.290456 WARNING::Fitting problem for feature 11 a warning was issued
2025-02-03 23:51:56.437342 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-03 23:51:56.575392 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-03 23:51:56.720784 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-03 23:51:56.879189 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-03 23:51:57.043808 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-03 23:51:57.167859 WARNING::Fitting problem for feature 16 a warning was issued
2025-02-03 23:51:57.333189 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-03 23:51:57.482035 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-03 23:51:57.667306 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-03 23:51:57.81797 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-03 23:51:57.970961 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-03 23:51:58.107812 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-03 23:51:58.242885 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-03 23:51:58.378329 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-03 23:51:58.511611 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-03 23:51:58.64277 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-03 23:51:58.784337 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-03 23:51:58.920133 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-03 23:51:59.047896 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-03 23:51:59.185415 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-03 23:51:59.326107 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-03 23:51:59.463372 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-03 23:51:59.612329 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-03 23:51:59.746838 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-03 23:51:59.880095 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-03 23:52:00.036602 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-03 23:52:00.17793 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-03 23:52:00.324383 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-03 23:52:00.476358 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-03 23:52:00.638774 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-03 23:52:00.786626 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-03 23:52:00.92883 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-03 23:52:01.07179 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-03 23:52:01.209867 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-03 23:52:01.355785 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-03 23:52:01.493285 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-03 23:52:01.633178 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-03 23:52:01.765026 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-03 23:52:01.913259 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-03 23:52:02.046208 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-03 23:52:02.178597 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-03 23:52:02.319614 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-03 23:52:02.456138 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-03 23:52:02.586475 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-03 23:52:02.720899 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-03 23:52:02.857297 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-03 23:52:03.014603 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-03 23:52:03.150034 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-03 23:52:03.29039 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-03 23:52:03.43105 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-03 23:52:03.580889 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-03 23:52:03.716295 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-03 23:52:03.846905 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-03 23:52:03.982717 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-03 23:52:04.117028 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-03 23:52:04.256478 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-03 23:52:04.386509 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-03 23:52:04.501116 WARNING::Fitting problem for feature 67 a warning was issued
2025-02-03 23:52:04.641976 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-03 23:52:04.777656 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-03 23:52:04.915954 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-03 23:52:05.058008 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-03 23:52:05.192091 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-03 23:52:05.239722 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-03 23:52:05.384061 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-03 23:52:05.517563 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-03 23:52:05.653521 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-03 23:52:05.790567 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-03 23:52:05.940997 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-03 23:52:06.076159 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-03 23:52:06.217408 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-03 23:52:06.373547 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-03 23:52:06.514007 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-03 23:52:06.660849 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-03 23:52:06.808339 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-03 23:52:06.955367 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-03 23:52:07.088123 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-03 23:52:07.229216 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-03 23:52:07.370746 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-03 23:52:07.543511 INFO::Counting total values for each feature
2025-02-03 23:52:07.565885 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-03 23:52:07.660498 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-03 23:52:07.757397 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-03 23:52:07.862762 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-03 23:52:07.92767 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-03 23:52:07.990144 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-03 23:52:07.995865 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-03 23:52:08.000662 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.517   0.627  31.133

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin289.623 0.89690.533