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

This page was generated on 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4756
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4475
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4435
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4390
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4383
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 1125/2275HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.21.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-01-04 07:40:27 -0000 (Sat, 04 Jan 2025)
EndedAt: 2025-01-04 07:43:55 -0000 (Sat, 04 Jan 2025)
EllapsedTime: 207.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 120.029  0.723 121.032
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘Maaslin2’ ...
** 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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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"
2025-01-04 07:43:05.561198 INFO::Writing function arguments to log file
2025-01-04 07:43:05.622458 INFO::Verifying options selected are valid
2025-01-04 07:43:05.672413 INFO::Determining format of input files
2025-01-04 07:43:05.674708 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-04 07:43:05.683353 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-04 07:43:05.685551 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-04 07:43:05.689554 INFO::Filter data based on min abundance and min prevalence
2025-01-04 07:43:05.691131 INFO::Total samples in data: 1595
2025-01-04 07:43:05.692602 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-04 07:43:05.703599 INFO::Total filtered features: 0
2025-01-04 07:43:05.705536 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-04 07:43:05.745791 INFO::Total filtered features with variance filtering: 0
2025-01-04 07:43:05.74765 INFO::Filtered feature names from variance filtering:
2025-01-04 07:43:05.749362 INFO::Running selected normalization method: TSS
2025-01-04 07:43:07.275884 INFO::Bypass z-score application to metadata
2025-01-04 07:43:07.277465 INFO::Running selected transform method: AST
2025-01-04 07:43:07.301739 INFO::Running selected analysis method: LM
2025-01-04 07:43:07.945525 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-04 07:43:08.432167 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-04 07:43:08.698133 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-04 07:43:08.940046 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-04 07:43:09.197558 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-04 07:43:09.431799 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-04 07:43:09.660577 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-04 07:43:09.897812 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-04 07:43:10.11675 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-04 07:43:10.3403 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-04 07:43:10.591734 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-04 07:43:10.875872 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-04 07:43:11.103094 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-04 07:43:11.344806 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-04 07:43:11.536982 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-04 07:43:12.083402 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-04 07:43:12.312114 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-04 07:43:12.55289 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-04 07:43:12.780463 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-04 07:43:13.028894 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-04 07:43:13.268522 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-04 07:43:13.488466 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-04 07:43:13.726099 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-04 07:43:13.964022 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-04 07:43:14.192073 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-04 07:43:14.407369 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-04 07:43:14.660428 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-04 07:43:14.892107 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-04 07:43:15.126148 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-04 07:43:15.386802 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-04 07:43:15.627898 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-04 07:43:15.873014 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-04 07:43:16.106314 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-04 07:43:16.339248 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-04 07:43:16.565004 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-04 07:43:16.813793 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-04 07:43:17.033125 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-04 07:43:17.258611 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-04 07:43:17.494741 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-04 07:43:17.723447 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-04 07:43:17.943518 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-04 07:43:18.179929 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-04 07:43:18.412869 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-04 07:43:18.639549 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-04 07:43:18.881269 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-04 07:43:19.104572 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-04 07:43:19.329631 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-04 07:43:19.560201 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-04 07:43:19.801892 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-04 07:43:20.052586 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-04 07:43:20.282151 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-04 07:43:20.532975 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-04 07:43:20.752304 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-04 07:43:20.974843 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-04 07:43:21.209277 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-04 07:43:21.465508 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-04 07:43:22.001551 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-04 07:43:22.237072 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-04 07:43:22.487338 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-04 07:43:22.722802 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-04 07:43:22.961801 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-04 07:43:23.193868 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-04 07:43:23.409998 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-04 07:43:23.643787 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-04 07:43:23.873358 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-04 07:43:24.099997 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-04 07:43:24.325186 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-04 07:43:24.540527 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-04 07:43:24.766612 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-04 07:43:24.990345 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-04 07:43:25.225307 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-04 07:43:25.461447 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-04 07:43:25.713195 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-04 07:43:25.942433 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-04 07:43:26.16036 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-04 07:43:26.39314 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-04 07:43:26.615815 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-04 07:43:26.839816 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-04 07:43:27.087761 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-04 07:43:27.317784 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-04 07:43:27.563095 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-04 07:43:27.821004 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-04 07:43:28.056364 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-04 07:43:28.293238 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-04 07:43:28.534416 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-04 07:43:28.748386 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-04 07:43:28.973215 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-04 07:43:29.201681 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-04 07:43:29.445817 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-04 07:43:29.759525 INFO::Counting total values for each feature
2025-01-04 07:43:29.828087 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-04 07:43:29.947066 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-04 07:43:30.065677 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-04 07:43:30.187631 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-04 07:43:30.245522 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-04 07:43:30.277339 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-04 07:43:30.284203 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-04 07:43:30.291239 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"
2025-01-04 07:43:30.309754 INFO::Writing function arguments to log file
2025-01-04 07:43:30.318555 INFO::Verifying options selected are valid
2025-01-04 07:43:30.329028 INFO::Determining format of input files
2025-01-04 07:43:30.331033 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-04 07:43:30.339252 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-04 07:43:30.341067 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-04 07:43:30.343616 INFO::Filter data based on min abundance and min prevalence
2025-01-04 07:43:30.345167 INFO::Total samples in data: 1595
2025-01-04 07:43:30.346645 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-04 07:43:30.356913 INFO::Total filtered features: 0
2025-01-04 07:43:30.35857 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-04 07:43:30.386879 INFO::Total filtered features with variance filtering: 0
2025-01-04 07:43:30.38864 INFO::Filtered feature names from variance filtering:
2025-01-04 07:43:30.390081 INFO::Running selected normalization method: NONE
2025-01-04 07:43:30.39141 INFO::Bypass z-score application to metadata
2025-01-04 07:43:30.392779 INFO::Running selected transform method: AST
2025-01-04 07:43:30.426598 INFO::Running selected analysis method: LM
2025-01-04 07:43:30.428931 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-04 07:43:30.65136 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-04 07:43:30.88746 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-04 07:43:31.095238 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-04 07:43:31.325844 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-04 07:43:31.537236 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-04 07:43:31.760636 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-04 07:43:31.982738 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-04 07:43:32.192343 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-04 07:43:32.703357 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-04 07:43:32.931076 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-04 07:43:33.157451 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-04 07:43:33.371946 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-04 07:43:33.59796 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-04 07:43:33.813524 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-04 07:43:34.045673 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-04 07:43:34.237834 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-04 07:43:34.459451 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-04 07:43:34.685244 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-04 07:43:34.90469 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-04 07:43:35.127219 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-04 07:43:35.356117 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-04 07:43:35.573779 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-04 07:43:35.790411 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-04 07:43:36.023675 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-04 07:43:36.246124 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-04 07:43:36.464236 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-04 07:43:36.684298 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-04 07:43:36.90193 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-04 07:43:37.110761 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-04 07:43:37.317225 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-04 07:43:37.539992 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-04 07:43:37.758857 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-04 07:43:37.988717 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-04 07:43:38.197881 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-04 07:43:38.43856 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-04 07:43:38.673657 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-04 07:43:38.900281 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-04 07:43:39.124307 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-04 07:43:39.341148 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-04 07:43:39.545742 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-04 07:43:39.765508 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-04 07:43:40.008482 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-04 07:43:40.23713 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-04 07:43:40.469448 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-04 07:43:40.7126 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-04 07:43:40.946659 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-04 07:43:41.19137 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-04 07:43:41.416415 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-04 07:43:41.633999 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-04 07:43:41.847545 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-04 07:43:42.05911 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-04 07:43:42.275484 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-04 07:43:42.473267 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-04 07:43:42.68824 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-04 07:43:42.905923 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-04 07:43:43.12413 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-04 07:43:43.343451 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-04 07:43:43.577939 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-04 07:43:43.789314 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-04 07:43:44.005427 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-04 07:43:44.219902 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-04 07:43:44.438497 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-04 07:43:44.653425 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-04 07:43:44.87239 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-04 07:43:45.099315 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-04 07:43:45.322606 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-04 07:43:45.536712 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-04 07:43:45.771113 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-04 07:43:45.987099 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-04 07:43:46.212976 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-04 07:43:46.454477 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-04 07:43:46.667213 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-04 07:43:46.743894 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-04 07:43:46.958377 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-04 07:43:47.190706 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-04 07:43:47.416312 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-04 07:43:47.633846 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-04 07:43:47.877186 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-04 07:43:48.096171 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-04 07:43:48.323063 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-04 07:43:48.552496 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-04 07:43:48.761621 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-04 07:43:49.001688 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-04 07:43:49.213818 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-04 07:43:49.425627 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-04 07:43:49.653851 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-04 07:43:49.863211 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-04 07:43:50.385971 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-04 07:43:50.643711 INFO::Counting total values for each feature
2025-01-04 07:43:50.680352 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-04 07:43:50.797537 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-04 07:43:50.916262 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-04 07:43:51.039547 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-04 07:43:51.118018 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-04 07:43:51.191882 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-04 07:43:51.198839 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-04 07:43:51.20537 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 46.500   0.583  47.188

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2120.029 0.723121.032