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

This page was generated on 2025-01-28 11:47 -0500 (Tue, 28 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4659
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4454
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4465
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4419
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4409
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: 2025-01-27 13:40 -0500 (Mon, 27 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: 2025-01-28 11:59:29 -0000 (Tue, 28 Jan 2025)
EndedAt: 2025-01-28 12:02:56 -0000 (Tue, 28 Jan 2025)
EllapsedTime: 206.2 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 120.884  0.926 122.097
* 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
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) (2024-11-24 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"
2025-01-28 12:02:07.703537 INFO::Writing function arguments to log file
2025-01-28 12:02:07.759099 INFO::Verifying options selected are valid
2025-01-28 12:02:07.803936 INFO::Determining format of input files
2025-01-28 12:02:07.805905 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-28 12:02:07.81328 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-28 12:02:07.815176 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-28 12:02:07.818506 INFO::Filter data based on min abundance and min prevalence
2025-01-28 12:02:07.819838 INFO::Total samples in data: 1595
2025-01-28 12:02:07.821084 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-28 12:02:07.830586 INFO::Total filtered features: 0
2025-01-28 12:02:07.832176 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-28 12:02:07.868695 INFO::Total filtered features with variance filtering: 0
2025-01-28 12:02:07.870173 INFO::Filtered feature names from variance filtering:
2025-01-28 12:02:07.871358 INFO::Running selected normalization method: TSS
2025-01-28 12:02:09.384172 INFO::Bypass z-score application to metadata
2025-01-28 12:02:09.386027 INFO::Running selected transform method: AST
2025-01-28 12:02:09.412201 INFO::Running selected analysis method: LM
2025-01-28 12:02:10.125117 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-28 12:02:10.617338 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-28 12:02:10.88449 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-28 12:02:11.118711 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-28 12:02:11.365154 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-28 12:02:11.59959 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-28 12:02:11.844107 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-28 12:02:12.082506 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-28 12:02:12.32706 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-28 12:02:12.583341 WARNING::Fitting problem for feature 9 a warning was issued
2025-01-28 12:02:12.981927 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-28 12:02:13.213961 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-28 12:02:13.443918 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-28 12:02:13.677894 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-28 12:02:13.871558 WARNING::Fitting problem for feature 13 a warning was issued
2025-01-28 12:02:14.1364 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-28 12:02:14.368868 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-28 12:02:14.613333 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-28 12:02:14.838385 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-28 12:02:15.093394 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-28 12:02:15.340861 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-28 12:02:15.582374 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-28 12:02:15.818849 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-28 12:02:16.068313 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-28 12:02:16.299413 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-28 12:02:16.51777 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-28 12:02:16.768126 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-28 12:02:17.007898 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-28 12:02:17.22955 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-28 12:02:17.477183 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-28 12:02:17.710967 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-28 12:02:17.955158 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-28 12:02:18.224576 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-28 12:02:18.479028 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-28 12:02:18.743443 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-28 12:02:18.983508 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-28 12:02:19.218987 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-28 12:02:19.475064 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-28 12:02:19.704046 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-28 12:02:19.942426 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-28 12:02:20.170501 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-28 12:02:20.400229 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-28 12:02:20.640784 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-28 12:02:20.865043 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-28 12:02:21.107727 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-28 12:02:21.329749 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-28 12:02:21.557726 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-28 12:02:21.789232 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-28 12:02:22.031998 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-28 12:02:22.65379 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-28 12:02:22.871131 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-28 12:02:23.098784 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-28 12:02:23.60574 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-28 12:02:23.826036 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-28 12:02:24.045674 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-28 12:02:24.280621 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-28 12:02:24.513938 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-28 12:02:24.750282 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-28 12:02:24.996642 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-28 12:02:25.23016 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-28 12:02:25.471179 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-28 12:02:25.700083 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-28 12:02:25.937087 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-28 12:02:26.167307 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-28 12:02:26.400379 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-28 12:02:26.649474 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-28 12:02:26.881794 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-28 12:02:27.101801 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-28 12:02:27.336371 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-28 12:02:27.572164 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-28 12:02:27.807812 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-28 12:02:28.071449 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-28 12:02:28.311086 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-28 12:02:28.544911 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-28 12:02:28.765656 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-28 12:02:28.98691 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-28 12:02:29.218345 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-28 12:02:29.454834 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-28 12:02:29.697501 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-28 12:02:29.931554 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-28 12:02:30.180244 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-28 12:02:30.437697 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-28 12:02:30.672159 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-28 12:02:30.94456 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-28 12:02:31.170465 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-28 12:02:31.39599 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-28 12:02:31.619557 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-28 12:02:31.843599 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-28 12:02:32.059485 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-28 12:02:32.351791 INFO::Counting total values for each feature
2025-01-28 12:02:32.402802 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-28 12:02:32.521583 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-28 12:02:32.638745 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-28 12:02:32.76966 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-28 12:02:32.82709 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-28 12:02:32.858801 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-28 12:02:32.865565 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-28 12:02:32.872226 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"
2025-01-28 12:02:32.889303 INFO::Writing function arguments to log file
2025-01-28 12:02:32.897369 INFO::Verifying options selected are valid
2025-01-28 12:02:32.898757 INFO::Determining format of input files
2025-01-28 12:02:32.900389 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-28 12:02:32.908453 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-28 12:02:32.910046 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-28 12:02:32.913058 INFO::Filter data based on min abundance and min prevalence
2025-01-28 12:02:32.914339 INFO::Total samples in data: 1595
2025-01-28 12:02:32.915727 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-28 12:02:32.924873 INFO::Total filtered features: 0
2025-01-28 12:02:32.926367 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-28 12:02:32.96267 INFO::Total filtered features with variance filtering: 0
2025-01-28 12:02:32.96427 INFO::Filtered feature names from variance filtering:
2025-01-28 12:02:32.96548 INFO::Running selected normalization method: NONE
2025-01-28 12:02:32.966615 INFO::Bypass z-score application to metadata
2025-01-28 12:02:32.967779 INFO::Running selected transform method: AST
2025-01-28 12:02:33.007396 INFO::Running selected analysis method: LM
2025-01-28 12:02:33.010658 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-28 12:02:33.218708 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-28 12:02:33.427572 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-28 12:02:33.639469 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-28 12:02:33.845437 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-28 12:02:34.067819 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-28 12:02:34.29462 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-28 12:02:34.519406 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-28 12:02:34.747865 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-28 12:02:34.960484 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-28 12:02:35.176578 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-28 12:02:35.404921 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-28 12:02:35.616976 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-28 12:02:35.828109 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-28 12:02:36.049911 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-28 12:02:36.262375 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-28 12:02:36.426944 WARNING::Fitting problem for feature 16 a warning was issued
2025-01-28 12:02:36.650469 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-28 12:02:36.861787 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-28 12:02:37.07008 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-28 12:02:37.28042 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-28 12:02:37.48925 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-28 12:02:37.713468 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-28 12:02:37.944567 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-28 12:02:38.160814 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-28 12:02:38.40355 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-28 12:02:38.633434 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-28 12:02:38.842068 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-28 12:02:39.074423 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-28 12:02:39.282615 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-28 12:02:39.49844 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-28 12:02:39.731922 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-28 12:02:39.943251 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-28 12:02:40.179162 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-28 12:02:40.399483 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-28 12:02:40.618871 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-28 12:02:40.859595 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-28 12:02:41.08357 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-28 12:02:41.311852 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-28 12:02:41.525714 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-28 12:02:41.748584 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-28 12:02:41.95668 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-28 12:02:42.166129 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-28 12:02:42.384966 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-28 12:02:42.597139 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-28 12:02:42.810423 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-28 12:02:43.045633 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-28 12:02:43.273874 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-28 12:02:43.486924 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-28 12:02:43.719039 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-28 12:02:43.925313 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-28 12:02:44.134471 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-28 12:02:44.347507 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-28 12:02:44.544362 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-28 12:02:44.753433 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-28 12:02:44.961491 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-28 12:02:45.183118 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-28 12:02:45.390159 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-28 12:02:45.597958 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-28 12:02:45.816568 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-28 12:02:46.03081 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-28 12:02:46.532362 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-28 12:02:46.74176 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-28 12:02:46.948398 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-28 12:02:47.160375 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-28 12:02:47.38193 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-28 12:02:47.595809 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-28 12:02:47.805223 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-28 12:02:48.029345 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-28 12:02:48.257903 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-28 12:02:48.476258 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-28 12:02:48.701209 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-28 12:02:48.912134 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-28 12:02:48.99716 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-28 12:02:49.208092 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-28 12:02:49.425658 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-28 12:02:49.639035 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-28 12:02:49.862143 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-28 12:02:50.09194 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-28 12:02:50.298079 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-28 12:02:50.503595 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-28 12:02:50.727653 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-28 12:02:50.932944 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-28 12:02:51.152128 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-28 12:02:51.361554 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-28 12:02:51.578434 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-28 12:02:51.786828 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-28 12:02:51.994387 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-28 12:02:52.212444 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-28 12:02:52.481889 INFO::Counting total values for each feature
2025-01-28 12:02:52.517773 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-28 12:02:52.632739 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-28 12:02:52.74823 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-28 12:02:52.869506 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-28 12:02:52.947045 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-28 12:02:53.020135 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-28 12:02:53.026873 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-28 12:02:53.03259 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 
 45.883   0.819  46.802

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2120.884 0.926122.097