Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1107/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on nebbiolo2

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: 1.19.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-06-25 00:19:24 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 00:23:25 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 241.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.19.0’
* 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 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 85.475  0.655  86.079
* 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-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.12
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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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"
2024-06-25 00:21:19.569572 INFO::Writing function arguments to log file
2024-06-25 00:21:19.61015 INFO::Verifying options selected are valid
2024-06-25 00:21:19.645917 INFO::Determining format of input files
2024-06-25 00:21:19.647294 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-25 00:21:19.651832 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-25 00:21:19.653075 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-25 00:21:19.655365 INFO::Filter data based on min abundance and min prevalence
2024-06-25 00:21:19.656185 INFO::Total samples in data: 1595
2024-06-25 00:21:19.657029 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-25 00:21:19.660636 INFO::Total filtered features: 0
2024-06-25 00:21:19.661574 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-25 00:21:19.674647 INFO::Total filtered features with variance filtering: 0
2024-06-25 00:21:19.675662 INFO::Filtered feature names from variance filtering:
2024-06-25 00:21:19.676515 INFO::Running selected normalization method: TSS
2024-06-25 00:21:20.87023 INFO::Bypass z-score application to metadata
2024-06-25 00:21:20.871681 INFO::Running selected transform method: AST
2024-06-25 00:21:20.888922 INFO::Running selected analysis method: LM
2024-06-25 00:21:21.365427 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-25 00:21:21.721588 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-25 00:21:21.869823 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-25 00:21:22.022557 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-25 00:21:22.176614 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-25 00:21:22.321197 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-25 00:21:22.465783 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-25 00:21:22.603507 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-25 00:21:22.719268 WARNING::Fitting problem for feature 8 a warning was issued
2024-06-25 00:21:22.866606 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-25 00:21:22.978603 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-25 00:21:23.145932 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-25 00:21:23.287849 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-25 00:21:23.433215 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-25 00:21:23.604579 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-25 00:21:23.722045 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-25 00:21:23.869816 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-25 00:21:24.012322 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-25 00:21:24.167667 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-25 00:21:24.316092 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-25 00:21:24.467887 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-25 00:21:24.638066 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-25 00:21:24.78795 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-25 00:21:24.939795 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-25 00:21:25.108379 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-25 00:21:25.255398 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-25 00:21:25.396444 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-25 00:21:25.541981 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-25 00:21:25.692098 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-25 00:21:25.830797 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-25 00:21:25.975799 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-25 00:21:26.124867 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-25 00:21:26.271102 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-25 00:21:26.40998 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-25 00:21:26.570406 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-25 00:21:26.714314 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-25 00:21:26.872554 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-25 00:21:27.02943 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-25 00:21:27.172144 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-25 00:21:27.315051 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-25 00:21:27.473097 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-25 00:21:27.620846 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-25 00:21:27.775459 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-25 00:21:27.92518 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-25 00:21:28.066199 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-25 00:21:28.223552 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-25 00:21:28.360161 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-25 00:21:28.544213 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-25 00:21:28.724208 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-25 00:21:28.866182 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-25 00:21:29.01747 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-25 00:21:29.154278 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-25 00:21:29.303216 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-25 00:21:29.456025 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-25 00:21:29.617112 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-25 00:21:29.759551 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-25 00:21:29.913045 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-25 00:21:30.048125 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-25 00:21:30.196988 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-25 00:21:30.346032 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-25 00:21:30.491968 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-25 00:21:30.640919 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-25 00:21:30.795116 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-25 00:21:30.984912 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-25 00:21:31.138774 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-25 00:21:31.297771 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-25 00:21:31.446383 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-25 00:21:31.589149 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-25 00:21:31.725712 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-25 00:21:31.867027 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-25 00:21:32.01827 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-25 00:21:32.163225 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-25 00:21:32.313349 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-25 00:21:32.692599 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-25 00:21:32.831107 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-25 00:21:32.966906 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-25 00:21:33.106209 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-25 00:21:33.24165 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-25 00:21:33.378971 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-25 00:21:33.736178 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-25 00:21:33.872364 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-25 00:21:34.06497 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-25 00:21:34.212811 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-25 00:21:34.365553 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-25 00:21:34.505719 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-25 00:21:34.645879 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-25 00:21:34.778363 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-25 00:21:34.915971 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-25 00:21:35.057872 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-25 00:21:35.19331 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-25 00:21:35.388843 INFO::Counting total values for each feature
2024-06-25 00:21:35.424809 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-25 00:21:35.57097 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-25 00:21:35.720762 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-25 00:21:35.872021 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-25 00:21:35.92921 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-25 00:21:36.251193 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-25 00:21:36.257927 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-25 00:21:36.264546 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"
2024-06-25 00:21:36.277708 INFO::Writing function arguments to log file
2024-06-25 00:21:36.283334 INFO::Verifying options selected are valid
2024-06-25 00:21:36.284261 INFO::Determining format of input files
2024-06-25 00:21:36.285381 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-25 00:21:36.290109 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-25 00:21:36.291073 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-25 00:21:36.292654 INFO::Filter data based on min abundance and min prevalence
2024-06-25 00:21:36.29346 INFO::Total samples in data: 1595
2024-06-25 00:21:36.29424 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-25 00:21:36.29779 INFO::Total filtered features: 0
2024-06-25 00:21:36.298653 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-25 00:21:36.304921 INFO::Total filtered features with variance filtering: 0
2024-06-25 00:21:36.305807 INFO::Filtered feature names from variance filtering:
2024-06-25 00:21:36.306571 INFO::Running selected normalization method: NONE
2024-06-25 00:21:36.307312 INFO::Bypass z-score application to metadata
2024-06-25 00:21:36.308078 INFO::Running selected transform method: AST
2024-06-25 00:21:36.323406 INFO::Running selected analysis method: LM
2024-06-25 00:21:36.325088 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-25 00:21:36.461169 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-25 00:21:36.592887 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-25 00:21:36.724147 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-25 00:21:36.863969 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-25 00:21:36.995299 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-25 00:21:37.130763 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-25 00:21:37.266572 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-25 00:21:37.404034 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-25 00:21:37.537565 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-25 00:21:37.676953 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-25 00:21:37.787899 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-25 00:21:37.932638 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-25 00:21:38.067342 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-25 00:21:38.201928 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-25 00:21:38.333701 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-25 00:21:38.467346 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-25 00:21:38.574758 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-25 00:21:38.7198 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-25 00:21:38.860221 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-25 00:21:39.000004 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-25 00:21:39.130478 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-25 00:21:39.28427 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-25 00:21:39.422284 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-25 00:21:39.55719 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-25 00:21:39.68895 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-25 00:21:39.831112 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-25 00:21:39.967522 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-25 00:21:40.100513 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-25 00:21:40.233133 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-25 00:21:40.359486 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-25 00:21:40.493782 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-25 00:21:40.623859 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-25 00:21:40.757046 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-25 00:21:40.890675 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-25 00:21:41.024374 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-25 00:21:41.154594 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-25 00:21:41.287024 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-25 00:21:41.422665 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-25 00:21:41.555236 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-25 00:21:41.694985 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-25 00:21:41.818719 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-25 00:21:41.942222 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-25 00:21:42.070281 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-25 00:21:42.203306 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-25 00:21:42.333862 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-25 00:21:42.467479 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-25 00:21:42.59841 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-25 00:21:42.733339 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-25 00:21:42.867647 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-25 00:21:43.001002 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-25 00:21:43.129047 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-25 00:21:43.248435 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-25 00:21:43.412038 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-25 00:21:43.53937 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-25 00:21:43.662611 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-25 00:21:43.794117 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-25 00:21:43.92886 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-25 00:21:44.059697 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-25 00:21:44.188013 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-25 00:21:44.317882 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-25 00:21:44.454915 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-25 00:21:44.583054 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-25 00:21:44.713479 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-25 00:21:44.841124 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-25 00:21:44.976692 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-25 00:21:45.103814 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-25 00:21:45.233274 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-25 00:21:45.359593 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-25 00:21:45.476774 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-25 00:21:45.615414 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-25 00:21:45.742769 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-25 00:21:45.88677 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-25 00:21:46.026423 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-25 00:21:46.156907 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-25 00:21:46.202001 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-25 00:21:46.353647 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-25 00:21:46.484116 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-25 00:21:46.616618 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-25 00:21:46.755482 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-25 00:21:46.893055 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-25 00:21:47.035615 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-25 00:21:47.167865 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-25 00:21:47.306015 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-25 00:21:47.439442 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-25 00:21:47.587879 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-25 00:21:47.71458 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-25 00:21:47.843873 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-25 00:21:47.97811 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-25 00:21:48.118542 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-25 00:21:48.269985 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-25 00:21:48.429383 INFO::Counting total values for each feature
2024-06-25 00:21:48.452181 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-25 00:21:48.595815 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-25 00:21:48.739943 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-25 00:21:48.891113 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-25 00:21:48.966266 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-25 00:21:49.038835 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-25 00:21:49.044638 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-25 00:21:49.050028 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 
 30.113   0.508  30.614

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin285.475 0.65586.079