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This page was generated on 2024-06-28 17:41 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 1138/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.18.0  (landing page)
Lauren McIver
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

CHECK results for Maaslin2 on palomino3

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: 1.18.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-06-27 03:08:13 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 03:11:48 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 215.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Maaslin2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '1.18.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'lme4' was built under R version 4.4.1
See 'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00install.out' for details.
* 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 113.74   7.48  121.82
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'lme4' was built under R version 4.4.1
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 (2024-04-24 ucrt) -- "Puppy Cup"
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"
2024-06-27 03:10:56.923879 INFO::Writing function arguments to log file
2024-06-27 03:10:56.98248 INFO::Verifying options selected are valid
2024-06-27 03:10:57.052788 INFO::Determining format of input files
2024-06-27 03:10:57.055334 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-27 03:10:57.069925 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-27 03:10:57.072375 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-27 03:10:57.075718 INFO::Filter data based on min abundance and min prevalence
2024-06-27 03:10:57.077674 INFO::Total samples in data: 1595
2024-06-27 03:10:57.079503 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-27 03:10:57.086026 INFO::Total filtered features: 0
2024-06-27 03:10:57.088226 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-27 03:10:57.09839 INFO::Total filtered features with variance filtering: 0
2024-06-27 03:10:57.100615 INFO::Filtered feature names from variance filtering:
2024-06-27 03:10:57.102545 INFO::Running selected normalization method: TSS
2024-06-27 03:10:58.458184 INFO::Bypass z-score application to metadata
2024-06-27 03:10:58.460409 INFO::Running selected transform method: AST
2024-06-27 03:10:58.479586 INFO::Running selected analysis method: LM
2024-06-27 03:10:58.896294 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-27 03:10:59.56098 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-27 03:10:59.788131 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-27 03:11:00.024675 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-27 03:11:00.183667 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-27 03:11:00.33277 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-27 03:11:00.489033 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-27 03:11:00.718074 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-27 03:11:00.928106 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-27 03:11:01.149498 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-27 03:11:01.385343 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-27 03:11:01.602358 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-27 03:11:01.759989 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-27 03:11:01.935935 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-27 03:11:02.176972 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-27 03:11:02.390072 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-27 03:11:02.621914 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-27 03:11:02.833796 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-27 03:11:03.079785 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-27 03:11:03.296901 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-27 03:11:03.489236 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-27 03:11:03.728311 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-27 03:11:03.958085 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-27 03:11:04.190413 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-27 03:11:04.398713 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-27 03:11:04.629055 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-27 03:11:04.856837 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-27 03:11:05.051895 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-27 03:11:05.210911 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-27 03:11:05.390883 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-27 03:11:05.582933 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-27 03:11:05.742912 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-27 03:11:05.991122 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-27 03:11:06.172377 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-27 03:11:06.329303 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-27 03:11:06.476492 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-27 03:11:06.867233 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-27 03:11:07.027827 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-27 03:11:07.227444 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-27 03:11:07.472323 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-27 03:11:07.686339 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-27 03:11:07.904722 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-27 03:11:08.128299 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-27 03:11:08.356277 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-27 03:11:08.498441 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-27 03:11:08.638719 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-27 03:11:08.787018 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-27 03:11:08.943286 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-27 03:11:09.142382 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-27 03:11:09.367408 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-27 03:11:09.577067 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-27 03:11:09.720612 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-27 03:11:09.872602 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-27 03:11:10.02352 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-27 03:11:10.221387 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-27 03:11:10.39949 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-27 03:11:10.581285 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-27 03:11:10.748274 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-27 03:11:11.12461 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-27 03:11:11.266708 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-27 03:11:11.43893 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-27 03:11:11.65207 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-27 03:11:11.831774 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-27 03:11:12.036362 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-27 03:11:12.185648 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-27 03:11:12.396529 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-27 03:11:12.569837 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-27 03:11:12.727578 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-27 03:11:12.882409 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-27 03:11:13.103642 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-27 03:11:13.305657 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-27 03:11:13.496888 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-27 03:11:13.684009 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-27 03:11:13.877424 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-27 03:11:14.113088 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-27 03:11:14.314463 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-27 03:11:14.499047 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-27 03:11:14.95636 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-27 03:11:15.16437 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-27 03:11:15.336538 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-27 03:11:15.586526 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-27 03:11:15.800689 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-27 03:11:15.98845 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-27 03:11:16.156869 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-27 03:11:16.361626 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-27 03:11:16.507213 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-27 03:11:16.718162 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-27 03:11:16.852929 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-27 03:11:17.105301 INFO::Counting total values for each feature
2024-06-27 03:11:17.153613 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-27 03:11:17.570559 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-27 03:11:18.043426 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-27 03:11:18.489023 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-27 03:11:18.561339 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-27 03:11:18.60127 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-27 03:11:18.611911 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-27 03:11:18.637171 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"
2024-06-27 03:11:18.679634 INFO::Writing function arguments to log file
2024-06-27 03:11:18.704527 INFO::Verifying options selected are valid
2024-06-27 03:11:18.70738 INFO::Determining format of input files
2024-06-27 03:11:18.710532 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-27 03:11:18.72226 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-27 03:11:18.725552 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-27 03:11:18.729767 INFO::Filter data based on min abundance and min prevalence
2024-06-27 03:11:18.732693 INFO::Total samples in data: 1595
2024-06-27 03:11:18.735524 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-27 03:11:18.74453 INFO::Total filtered features: 0
2024-06-27 03:11:18.747673 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-27 03:11:18.758691 INFO::Total filtered features with variance filtering: 0
2024-06-27 03:11:18.761162 INFO::Filtered feature names from variance filtering:
2024-06-27 03:11:18.763064 INFO::Running selected normalization method: NONE
2024-06-27 03:11:18.765012 INFO::Bypass z-score application to metadata
2024-06-27 03:11:18.766871 INFO::Running selected transform method: AST
2024-06-27 03:11:18.794186 INFO::Running selected analysis method: LM
2024-06-27 03:11:18.797015 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-27 03:11:18.952987 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-27 03:11:19.418422 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-27 03:11:19.610355 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-27 03:11:19.762122 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-27 03:11:19.913619 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-27 03:11:20.11142 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-27 03:11:20.274644 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-27 03:11:20.438052 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-27 03:11:20.603178 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-27 03:11:20.794101 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-27 03:11:21.009282 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-27 03:11:21.188068 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-27 03:11:21.411202 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-27 03:11:21.600218 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-27 03:11:21.801837 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-27 03:11:21.92995 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-27 03:11:22.113985 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-27 03:11:22.274793 WARNING::Fitting problem for feature 16 a warning was issued
2024-06-27 03:11:22.491449 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-27 03:11:22.698418 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-27 03:11:22.834867 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-27 03:11:22.968684 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-27 03:11:23.107127 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-27 03:11:23.259108 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-27 03:11:23.403594 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-27 03:11:23.533832 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-27 03:11:23.983646 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-27 03:11:24.202987 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-27 03:11:24.41371 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-27 03:11:24.632383 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-27 03:11:24.862384 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-27 03:11:25.048668 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-27 03:11:25.246325 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-27 03:11:25.45223 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-27 03:11:25.928185 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-27 03:11:26.125084 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-27 03:11:26.323555 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-27 03:11:26.461486 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-27 03:11:26.667781 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-27 03:11:26.879145 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-27 03:11:27.035466 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-27 03:11:27.18063 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-27 03:11:27.32897 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-27 03:11:27.534646 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-27 03:11:27.74638 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-27 03:11:27.987995 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-27 03:11:28.213169 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-27 03:11:28.429111 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-27 03:11:28.651395 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-27 03:11:28.866518 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-27 03:11:29.089879 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-27 03:11:29.289039 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-27 03:11:29.53705 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-27 03:11:29.773881 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-27 03:11:29.98247 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-27 03:11:30.173862 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-27 03:11:30.40298 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-27 03:11:30.620187 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-27 03:11:30.795897 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-27 03:11:30.986842 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-27 03:11:31.189511 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-27 03:11:31.389997 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-27 03:11:31.572384 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-27 03:11:31.991785 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-27 03:11:32.126652 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-27 03:11:32.27536 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-27 03:11:32.431215 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-27 03:11:32.577481 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-27 03:11:32.70986 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-27 03:11:32.91381 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-27 03:11:33.059543 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-27 03:11:33.266585 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-27 03:11:33.480238 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-27 03:11:33.675038 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-27 03:11:33.740253 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-27 03:11:33.914116 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-27 03:11:34.08247 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-27 03:11:34.257857 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-27 03:11:34.472078 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-27 03:11:34.694243 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-27 03:11:34.895032 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-27 03:11:35.051731 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-27 03:11:35.235157 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-27 03:11:35.450733 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-27 03:11:35.632916 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-27 03:11:35.809731 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-27 03:11:35.98552 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-27 03:11:36.190866 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-27 03:11:36.401593 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-27 03:11:36.608815 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-27 03:11:36.817911 INFO::Counting total values for each feature
2024-06-27 03:11:36.844261 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-27 03:11:37.254675 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-27 03:11:37.747223 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-27 03:11:38.207016 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-27 03:11:38.286862 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-27 03:11:38.362433 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-27 03:11:38.37246 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-27 03:11:38.386901 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 
  41.46    1.43   43.64

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2113.74 7.48121.82