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This page was generated on 2024-03-04 11:37:30 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1124/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.16.0  (landing page)
Lauren McIver
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_18
git_last_commit: 0ab531d
git_last_commit_date: 2023-10-24 11:15:22 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for Maaslin2 on lconway


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: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.16.0.tar.gz
StartedAt: 2024-03-03 21:30:52 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 21:33:57 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 185.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.16.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 97.876  2.009 100.628
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 1.9.6
Current TMB version is 1.9.10
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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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"
2024-03-03 21:33:14.228008 INFO::Writing function arguments to log file
2024-03-03 21:33:14.288331 INFO::Verifying options selected are valid
2024-03-03 21:33:14.327714 INFO::Determining format of input files
2024-03-03 21:33:14.329282 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-03 21:33:14.33674 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-03 21:33:14.338858 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-03-03 21:33:14.341714 INFO::Filter data based on min abundance and min prevalence
2024-03-03 21:33:14.342708 INFO::Total samples in data: 1595
2024-03-03 21:33:14.343612 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-03 21:33:14.348008 INFO::Total filtered features: 0
2024-03-03 21:33:14.349116 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-03 21:33:14.358585 INFO::Total filtered features with variance filtering: 0
2024-03-03 21:33:14.360409 INFO::Filtered feature names from variance filtering:
2024-03-03 21:33:14.361829 INFO::Running selected normalization method: TSS
2024-03-03 21:33:15.668846 INFO::Bypass z-score application to metadata
2024-03-03 21:33:15.670203 INFO::Running selected transform method: AST
2024-03-03 21:33:15.685912 INFO::Running selected analysis method: LM
2024-03-03 21:33:16.324741 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-03 21:33:16.717634 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-03 21:33:16.928395 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-03 21:33:17.097233 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-03 21:33:17.258755 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-03 21:33:17.430047 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-03 21:33:17.601165 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-03 21:33:17.753318 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-03 21:33:17.906162 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-03 21:33:18.047572 WARNING::Fitting problem for feature 9 a warning was issued
2024-03-03 21:33:18.217194 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-03 21:33:18.39064 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-03 21:33:18.563572 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-03 21:33:18.7642 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-03 21:33:18.900257 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-03 21:33:19.097067 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-03 21:33:19.26379 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-03 21:33:19.434375 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-03 21:33:19.585782 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-03 21:33:19.756349 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-03 21:33:19.951128 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-03 21:33:20.125263 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-03 21:33:20.288458 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-03 21:33:20.469566 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-03 21:33:20.643184 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-03 21:33:20.784194 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-03 21:33:20.956664 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-03 21:33:21.131776 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-03 21:33:21.295387 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-03 21:33:21.470171 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-03 21:33:21.636406 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-03 21:33:21.79903 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-03 21:33:21.982149 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-03 21:33:22.161002 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-03 21:33:22.329328 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-03 21:33:22.490711 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-03 21:33:22.629063 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-03 21:33:22.798236 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-03 21:33:22.979469 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-03 21:33:23.159692 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-03 21:33:23.335064 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-03 21:33:23.489091 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-03 21:33:23.664222 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-03 21:33:23.838606 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-03 21:33:24.015845 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-03 21:33:24.19296 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-03 21:33:24.346751 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-03 21:33:24.513502 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-03 21:33:24.673074 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-03 21:33:24.833912 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-03 21:33:24.991391 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-03 21:33:25.149156 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-03 21:33:25.31026 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-03 21:33:25.46288 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-03 21:33:25.636235 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-03 21:33:25.811387 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-03 21:33:25.960065 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-03 21:33:26.101944 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-03 21:33:26.296212 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-03 21:33:26.471449 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-03 21:33:26.614899 WARNING::Fitting problem for feature 58 a warning was issued
2024-03-03 21:33:26.794634 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-03 21:33:26.954864 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-03 21:33:27.130842 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-03 21:33:27.51719 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-03 21:33:27.691298 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-03 21:33:27.869535 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-03 21:33:28.040921 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-03 21:33:28.192412 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-03 21:33:28.369602 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-03 21:33:28.508499 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-03 21:33:28.695483 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-03 21:33:28.850194 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-03 21:33:29.026473 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-03 21:33:29.18831 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-03 21:33:29.340622 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-03 21:33:29.505839 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-03 21:33:29.667746 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-03 21:33:29.810913 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-03 21:33:29.990297 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-03 21:33:30.113243 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-03 21:33:30.267529 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-03 21:33:30.419566 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-03 21:33:30.571905 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-03 21:33:30.736282 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-03 21:33:30.912915 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-03 21:33:31.066366 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-03 21:33:31.227571 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-03 21:33:31.362341 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-03 21:33:31.489548 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-03 21:33:31.655935 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-03 21:33:31.856543 INFO::Counting total values for each feature
2024-03-03 21:33:31.895375 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-03-03 21:33:32.035835 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-03-03 21:33:32.186036 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-03-03 21:33:32.342716 INFO::Writing residuals to file output/fits/residuals.rds
2024-03-03 21:33:32.392627 INFO::Writing fitted values to file output/fits/fitted.rds
2024-03-03 21:33:32.420066 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-03-03 21:33:32.427878 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-03-03 21:33:32.437631 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"
2024-03-03 21:33:32.456464 INFO::Writing function arguments to log file
2024-03-03 21:33:32.463652 INFO::Verifying options selected are valid
2024-03-03 21:33:32.46478 INFO::Determining format of input files
2024-03-03 21:33:32.466423 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-03 21:33:32.47232 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-03 21:33:32.473495 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-03-03 21:33:32.475812 INFO::Filter data based on min abundance and min prevalence
2024-03-03 21:33:32.477136 INFO::Total samples in data: 1595
2024-03-03 21:33:32.478359 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-03 21:33:32.483047 INFO::Total filtered features: 0
2024-03-03 21:33:32.484596 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-03 21:33:32.505768 INFO::Total filtered features with variance filtering: 0
2024-03-03 21:33:32.507911 INFO::Filtered feature names from variance filtering:
2024-03-03 21:33:32.50916 INFO::Running selected normalization method: NONE
2024-03-03 21:33:32.51061 INFO::Bypass z-score application to metadata
2024-03-03 21:33:32.511936 INFO::Running selected transform method: AST
2024-03-03 21:33:32.532221 INFO::Running selected analysis method: LM
2024-03-03 21:33:32.534552 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-03 21:33:32.702057 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-03 21:33:32.851012 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-03 21:33:32.997314 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-03 21:33:33.129178 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-03 21:33:33.282661 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-03 21:33:33.43805 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-03 21:33:33.583156 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-03 21:33:33.772675 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-03 21:33:33.931587 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-03 21:33:34.088328 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-03 21:33:34.24443 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-03 21:33:34.401335 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-03 21:33:34.538658 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-03 21:33:34.705909 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-03 21:33:34.869189 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-03 21:33:35.049664 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-03 21:33:35.193921 WARNING::Fitting problem for feature 16 a warning was issued
2024-03-03 21:33:35.356553 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-03 21:33:35.531255 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-03 21:33:35.71869 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-03 21:33:35.876567 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-03 21:33:36.049814 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-03 21:33:36.211679 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-03 21:33:36.385772 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-03 21:33:36.770708 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-03 21:33:36.933272 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-03 21:33:37.100759 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-03 21:33:37.271737 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-03 21:33:37.4528 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-03 21:33:37.606455 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-03 21:33:37.755444 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-03 21:33:37.926038 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-03 21:33:38.098565 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-03 21:33:38.261208 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-03 21:33:38.405807 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-03 21:33:38.578474 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-03 21:33:38.736231 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-03 21:33:38.887145 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-03 21:33:39.034777 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-03 21:33:39.20167 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-03 21:33:39.338858 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-03 21:33:39.485808 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-03 21:33:39.648371 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-03 21:33:39.814331 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-03 21:33:39.980695 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-03 21:33:40.145685 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-03 21:33:40.311916 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-03 21:33:40.470152 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-03 21:33:40.627036 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-03 21:33:41.032813 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-03 21:33:41.185036 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-03 21:33:41.339961 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-03 21:33:41.501566 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-03 21:33:41.657994 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-03 21:33:41.831724 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-03 21:33:41.994655 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-03 21:33:42.155841 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-03 21:33:42.327443 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-03 21:33:42.481106 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-03 21:33:42.662983 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-03 21:33:42.808332 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-03 21:33:42.970033 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-03 21:33:43.126538 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-03 21:33:43.292811 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-03 21:33:43.469037 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-03 21:33:43.633554 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-03 21:33:43.799678 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-03 21:33:43.960369 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-03 21:33:44.096381 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-03 21:33:44.283444 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-03 21:33:44.453604 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-03 21:33:44.645848 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-03 21:33:44.832642 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-03 21:33:44.997563 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-03 21:33:45.054705 WARNING::Fitting problem for feature 72 a warning was issued
2024-03-03 21:33:45.228915 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-03 21:33:45.409146 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-03 21:33:45.584823 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-03 21:33:45.74176 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-03 21:33:45.912923 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-03 21:33:46.048357 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-03 21:33:46.194989 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-03 21:33:46.356301 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-03 21:33:46.507309 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-03 21:33:46.679384 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-03 21:33:46.830766 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-03 21:33:46.982191 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-03 21:33:47.14772 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-03 21:33:47.31592 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-03 21:33:47.482902 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-03 21:33:47.678544 INFO::Counting total values for each feature
2024-03-03 21:33:47.706634 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-03-03 21:33:47.849091 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-03-03 21:33:47.971436 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-03-03 21:33:48.142686 INFO::Writing residuals to file output2/fits/residuals.rds
2024-03-03 21:33:48.226985 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-03-03 21:33:48.318222 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-03-03 21:33:48.326581 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-03-03 21:33:48.335751 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 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 34.536   0.891  35.686

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 97.876 2.009100.628