Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1108/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 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
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

CHECK results for Maaslin2 on palomino6

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: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-07-16 01:19:02 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 01:21:43 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 161.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 84.72   7.27   91.72
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 1.9.12
Current TMB version is 1.9.14
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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2024-07-16 01:21:07.813711 INFO::Writing function arguments to log file
2024-07-16 01:21:07.868101 INFO::Verifying options selected are valid
2024-07-16 01:21:07.897877 INFO::Determining format of input files
2024-07-16 01:21:07.900361 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-16 01:21:07.915596 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-16 01:21:07.91887 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-16 01:21:07.922019 INFO::Filter data based on min abundance and min prevalence
2024-07-16 01:21:07.923651 INFO::Total samples in data: 1595
2024-07-16 01:21:07.925237 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-16 01:21:07.929969 INFO::Total filtered features: 0
2024-07-16 01:21:07.931894 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-16 01:21:07.941697 INFO::Total filtered features with variance filtering: 0
2024-07-16 01:21:07.94366 INFO::Filtered feature names from variance filtering:
2024-07-16 01:21:07.94536 INFO::Running selected normalization method: TSS
2024-07-16 01:21:09.145115 INFO::Bypass z-score application to metadata
2024-07-16 01:21:09.147895 INFO::Running selected transform method: AST
2024-07-16 01:21:09.16719 INFO::Running selected analysis method: LM
2024-07-16 01:21:09.446627 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-16 01:21:09.788409 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-16 01:21:09.920482 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-16 01:21:10.051068 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-16 01:21:10.179185 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-16 01:21:10.314137 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-16 01:21:10.439942 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-16 01:21:10.609413 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-16 01:21:10.733224 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-16 01:21:10.863148 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-16 01:21:10.997572 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-16 01:21:11.10855 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-16 01:21:11.222289 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-16 01:21:11.318815 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-16 01:21:11.458212 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-16 01:21:11.574205 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-16 01:21:11.70585 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-16 01:21:11.835378 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-16 01:21:11.972671 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-16 01:21:12.097023 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-16 01:21:12.213184 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-16 01:21:12.334162 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-16 01:21:12.458818 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-16 01:21:12.583987 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-16 01:21:13.297859 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-16 01:21:13.426745 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-16 01:21:13.555484 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-16 01:21:13.676669 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-16 01:21:13.796797 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-16 01:21:13.918132 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-16 01:21:14.041504 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-16 01:21:14.189978 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-16 01:21:14.312838 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-16 01:21:14.682715 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-16 01:21:14.808529 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-16 01:21:14.929168 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-16 01:21:15.074736 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-16 01:21:15.191689 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-16 01:21:15.309767 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-16 01:21:15.421815 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-16 01:21:15.54411 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-16 01:21:15.666643 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-16 01:21:15.786613 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-16 01:21:15.916608 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-16 01:21:16.026533 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-16 01:21:16.13902 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-16 01:21:16.260563 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-16 01:21:16.376415 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-16 01:21:16.498255 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-16 01:21:16.621328 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-16 01:21:16.73336 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-16 01:21:16.844965 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-16 01:21:16.965591 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-16 01:21:17.080125 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-16 01:21:17.200205 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-16 01:21:17.317179 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-16 01:21:17.436838 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-16 01:21:17.56683 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-16 01:21:17.975761 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-16 01:21:18.093759 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-16 01:21:18.213679 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-16 01:21:18.340222 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-16 01:21:18.456896 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-16 01:21:18.574302 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-16 01:21:18.710252 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-16 01:21:18.82627 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-16 01:21:18.94757 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-16 01:21:19.075748 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-16 01:21:19.185186 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-16 01:21:20.014312 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-16 01:21:20.155554 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-16 01:21:20.284712 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-16 01:21:20.403612 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-16 01:21:20.530626 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-16 01:21:20.647732 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-16 01:21:20.776506 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-16 01:21:20.904173 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-16 01:21:21.023346 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-16 01:21:21.147943 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-16 01:21:21.27812 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-16 01:21:21.405982 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-16 01:21:21.535787 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-16 01:21:21.670791 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-16 01:21:21.800999 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-16 01:21:21.919077 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-16 01:21:22.04576 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-16 01:21:22.177256 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-16 01:21:22.296292 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-16 01:21:22.460477 INFO::Counting total values for each feature
2024-07-16 01:21:22.501819 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-16 01:21:22.810544 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-16 01:21:23.1666 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-16 01:21:23.521459 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-16 01:21:23.562563 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-16 01:21:23.586288 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-16 01:21:23.592279 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-16 01:21:23.607622 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"
2024-07-16 01:21:23.635234 INFO::Writing function arguments to log file
2024-07-16 01:21:23.651869 INFO::Verifying options selected are valid
2024-07-16 01:21:23.653997 INFO::Determining format of input files
2024-07-16 01:21:23.655859 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-16 01:21:23.663233 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-16 01:21:23.665111 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-16 01:21:23.667598 INFO::Filter data based on min abundance and min prevalence
2024-07-16 01:21:23.669214 INFO::Total samples in data: 1595
2024-07-16 01:21:23.67078 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-16 01:21:23.675993 INFO::Total filtered features: 0
2024-07-16 01:21:23.677694 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-16 01:21:23.687698 INFO::Total filtered features with variance filtering: 0
2024-07-16 01:21:23.68969 INFO::Filtered feature names from variance filtering:
2024-07-16 01:21:23.691371 INFO::Running selected normalization method: NONE
2024-07-16 01:21:23.692944 INFO::Bypass z-score application to metadata
2024-07-16 01:21:23.694536 INFO::Running selected transform method: AST
2024-07-16 01:21:23.717858 INFO::Running selected analysis method: LM
2024-07-16 01:21:23.720465 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-16 01:21:23.852436 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-16 01:21:23.974545 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-16 01:21:24.092695 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-16 01:21:24.23931 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-16 01:21:24.355789 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-16 01:21:24.478622 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-16 01:21:24.614014 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-16 01:21:24.734407 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-16 01:21:24.834944 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-16 01:21:24.985464 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-16 01:21:25.106611 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-16 01:21:25.206017 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-16 01:21:25.343993 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-16 01:21:25.46271 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-16 01:21:25.575042 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-16 01:21:25.695875 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-16 01:21:25.808927 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-16 01:21:25.90712 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-16 01:21:26.023689 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-16 01:21:26.675845 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-16 01:21:26.802372 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-16 01:21:26.915169 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-16 01:21:27.053862 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-16 01:21:27.165813 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-16 01:21:27.278723 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-16 01:21:27.416428 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-16 01:21:27.535297 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-16 01:21:27.651907 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-16 01:21:27.78316 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-16 01:21:27.900989 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-16 01:21:28.015613 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-16 01:21:28.139673 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-16 01:21:28.260247 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-16 01:21:28.387201 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-16 01:21:28.506079 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-16 01:21:28.611032 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-16 01:21:28.736054 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-16 01:21:28.844161 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-16 01:21:28.955597 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-16 01:21:29.085775 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-16 01:21:29.199754 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-16 01:21:29.313284 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-16 01:21:29.447994 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-16 01:21:29.568285 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-16 01:21:29.680471 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-16 01:21:29.809704 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-16 01:21:29.930168 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-16 01:21:30.068128 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-16 01:21:30.188634 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-16 01:21:30.297586 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-16 01:21:30.424068 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-16 01:21:30.532271 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-16 01:21:30.639989 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-16 01:21:30.76851 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-16 01:21:30.87489 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-16 01:21:30.992696 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-16 01:21:31.104785 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-16 01:21:31.236476 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-16 01:21:31.345558 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-16 01:21:31.451198 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-16 01:21:31.57792 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-16 01:21:31.687292 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-16 01:21:31.801312 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-16 01:21:31.904607 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-16 01:21:32.023658 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-16 01:21:32.134136 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-16 01:21:32.254801 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-16 01:21:32.366122 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-16 01:21:32.487174 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-16 01:21:32.607788 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-16 01:21:32.715792 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-16 01:21:32.841169 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-16 01:21:32.955679 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-16 01:21:33.087321 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-16 01:21:33.125384 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-16 01:21:33.232014 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-16 01:21:33.65457 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-16 01:21:33.765367 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-16 01:21:33.874939 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-16 01:21:33.997467 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-16 01:21:34.104008 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-16 01:21:34.230406 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-16 01:21:34.338232 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-16 01:21:34.445477 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-16 01:21:34.573246 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-16 01:21:34.682154 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-16 01:21:34.793139 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-16 01:21:34.916633 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-16 01:21:35.028225 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-16 01:21:35.167945 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-16 01:21:35.304239 INFO::Counting total values for each feature
2024-07-16 01:21:35.341801 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-16 01:21:35.653066 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-16 01:21:35.968914 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-16 01:21:36.314323 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-16 01:21:36.366473 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-16 01:21:36.415847 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-16 01:21:36.422103 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-16 01:21:36.434169 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  28.85    2.14   30.96

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin284.72 7.2791.72