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This page was generated on 2024-04-17 11:37:53 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 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 -0400 (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
merida1macOS 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 merida1


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: 2024-04-16 04:43:26 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 04:49:18 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 352.1 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 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 171.943  2.891 197.073
* 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 1.9.10
Current TMB version is 1.9.11
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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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"
2024-04-16 04:47:57.729741 INFO::Writing function arguments to log file
2024-04-16 04:47:57.825075 INFO::Verifying options selected are valid
2024-04-16 04:47:57.907302 INFO::Determining format of input files
2024-04-16 04:47:57.910262 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-16 04:47:57.923548 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-16 04:47:57.928811 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-04-16 04:47:57.934433 INFO::Filter data based on min abundance and min prevalence
2024-04-16 04:47:57.938383 INFO::Total samples in data: 1595
2024-04-16 04:47:57.940811 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-16 04:47:57.953065 INFO::Total filtered features: 0
2024-04-16 04:47:57.955855 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-16 04:47:57.978107 INFO::Total filtered features with variance filtering: 0
2024-04-16 04:47:57.980681 INFO::Filtered feature names from variance filtering:
2024-04-16 04:47:57.98373 INFO::Running selected normalization method: TSS
2024-04-16 04:48:00.635751 INFO::Bypass z-score application to metadata
2024-04-16 04:48:00.638348 INFO::Running selected transform method: AST
2024-04-16 04:48:00.682457 INFO::Running selected analysis method: LM
2024-04-16 04:48:01.86269 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-16 04:48:02.703552 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-16 04:48:03.119124 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-16 04:48:03.454198 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-16 04:48:03.799755 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-16 04:48:04.142769 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-16 04:48:04.484624 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-16 04:48:04.812238 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-16 04:48:05.14388 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-16 04:48:05.482905 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-16 04:48:05.801556 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-16 04:48:06.129625 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-16 04:48:06.444848 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-16 04:48:06.770827 WARNING::Fitting problem for feature 13 a warning was issued
2024-04-16 04:48:07.117461 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-16 04:48:07.429302 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-16 04:48:07.783904 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-16 04:48:08.09499 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-16 04:48:08.572489 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-16 04:48:09.055893 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-16 04:48:09.374327 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-16 04:48:09.747745 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-16 04:48:10.083994 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-16 04:48:10.429814 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-16 04:48:10.747146 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-16 04:48:11.06113 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-16 04:48:11.402158 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-16 04:48:11.731005 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-16 04:48:12.066926 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-16 04:48:12.406672 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-16 04:48:12.751564 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-16 04:48:13.07086 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-16 04:48:13.420998 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-16 04:48:13.819057 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-16 04:48:14.24399 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-16 04:48:14.582753 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-16 04:48:14.897715 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-16 04:48:15.253225 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-16 04:48:15.565982 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-16 04:48:15.879873 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-16 04:48:16.201543 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-16 04:48:16.521553 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-16 04:48:16.857173 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-16 04:48:17.18847 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-16 04:48:17.547946 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-16 04:48:17.871347 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-16 04:48:18.189834 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-16 04:48:18.533558 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-16 04:48:18.865849 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-16 04:48:19.201244 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-16 04:48:19.53267 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-16 04:48:19.864225 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-16 04:48:20.185668 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-16 04:48:20.794591 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-16 04:48:21.137108 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-16 04:48:21.442139 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-16 04:48:21.77555 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-16 04:48:22.114607 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-16 04:48:22.420953 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-16 04:48:22.748999 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-16 04:48:23.075623 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-16 04:48:23.394357 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-16 04:48:23.708091 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-16 04:48:24.047756 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-16 04:48:24.367543 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-16 04:48:24.684064 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-16 04:48:25.01409 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-16 04:48:25.333791 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-16 04:48:25.63724 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-16 04:48:25.977188 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-16 04:48:26.309722 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-16 04:48:26.643756 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-16 04:48:26.964742 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-16 04:48:27.28542 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-16 04:48:27.884548 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-16 04:48:28.184737 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-16 04:48:28.514172 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-16 04:48:28.840245 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-16 04:48:29.172006 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-16 04:48:29.525459 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-16 04:48:29.865265 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-16 04:48:30.203671 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-16 04:48:30.531487 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-16 04:48:30.862414 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-16 04:48:31.186989 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-16 04:48:31.572632 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-16 04:48:31.891788 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-16 04:48:32.223231 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-16 04:48:32.667002 INFO::Counting total values for each feature
2024-04-16 04:48:32.758658 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-04-16 04:48:33.053901 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-04-16 04:48:33.417548 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-04-16 04:48:33.801069 INFO::Writing residuals to file output/fits/residuals.rds
2024-04-16 04:48:33.90202 INFO::Writing fitted values to file output/fits/fitted.rds
2024-04-16 04:48:33.955554 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-04-16 04:48:33.96767 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-04-16 04:48:33.987692 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"
2024-04-16 04:48:34.019155 INFO::Writing function arguments to log file
2024-04-16 04:48:34.036501 INFO::Verifying options selected are valid
2024-04-16 04:48:34.038907 INFO::Determining format of input files
2024-04-16 04:48:34.042903 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-16 04:48:34.056506 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-16 04:48:34.059238 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-04-16 04:48:34.06408 INFO::Filter data based on min abundance and min prevalence
2024-04-16 04:48:34.06686 INFO::Total samples in data: 1595
2024-04-16 04:48:34.069265 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-16 04:48:34.080312 INFO::Total filtered features: 0
2024-04-16 04:48:34.083208 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-16 04:48:34.101467 INFO::Total filtered features with variance filtering: 0
2024-04-16 04:48:34.104089 INFO::Filtered feature names from variance filtering:
2024-04-16 04:48:34.106386 INFO::Running selected normalization method: NONE
2024-04-16 04:48:34.112013 INFO::Bypass z-score application to metadata
2024-04-16 04:48:34.11446 INFO::Running selected transform method: AST
2024-04-16 04:48:34.148486 INFO::Running selected analysis method: LM
2024-04-16 04:48:34.151771 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-16 04:48:34.47692 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-16 04:48:34.79707 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-16 04:48:35.126747 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-16 04:48:35.443383 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-16 04:48:35.749782 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-16 04:48:36.087626 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-16 04:48:36.40655 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-16 04:48:36.740602 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-16 04:48:37.094417 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-16 04:48:37.410933 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-16 04:48:37.743348 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-16 04:48:38.058616 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-16 04:48:38.340557 WARNING::Fitting problem for feature 13 a warning was issued
2024-04-16 04:48:38.690691 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-16 04:48:38.996459 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-16 04:48:39.299915 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-16 04:48:39.597274 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-16 04:48:39.899927 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-16 04:48:40.223827 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-16 04:48:40.510449 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-16 04:48:40.827392 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-16 04:48:41.135921 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-16 04:48:41.432976 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-16 04:48:41.736498 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-16 04:48:42.050691 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-16 04:48:42.347741 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-16 04:48:42.634217 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-16 04:48:42.936515 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-16 04:48:43.227567 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-16 04:48:43.554645 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-16 04:48:43.850059 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-16 04:48:44.13938 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-16 04:48:44.458538 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-16 04:48:44.731037 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-16 04:48:45.022394 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-16 04:48:45.321973 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-16 04:48:45.636477 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-16 04:48:45.954694 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-16 04:48:46.314565 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-16 04:48:46.618651 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-16 04:48:46.934508 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-16 04:48:47.246037 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-16 04:48:47.543514 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-16 04:48:47.878202 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-16 04:48:48.175632 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-16 04:48:48.476209 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-16 04:48:48.803706 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-16 04:48:49.093346 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-16 04:48:49.401727 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-16 04:48:49.714833 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-16 04:48:50.005718 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-16 04:48:50.32474 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-16 04:48:50.628374 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-16 04:48:50.943631 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-16 04:48:51.254976 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-16 04:48:51.554794 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-16 04:48:51.865113 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-16 04:48:52.173933 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-16 04:48:52.474772 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-16 04:48:52.801887 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-16 04:48:53.09488 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-16 04:48:53.396104 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-16 04:48:53.709076 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-16 04:48:54.013322 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-16 04:48:54.314632 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-16 04:48:54.618824 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-16 04:48:54.927238 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-16 04:48:55.18233 WARNING::Fitting problem for feature 67 a warning was issued
2024-04-16 04:48:55.516811 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-16 04:48:55.803731 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-16 04:48:56.114633 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-16 04:48:56.443539 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-16 04:48:56.779898 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-16 04:48:56.885199 WARNING::Fitting problem for feature 72 a warning was issued
2024-04-16 04:48:57.256588 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-16 04:48:57.593829 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-16 04:48:57.942497 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-16 04:48:58.246783 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-16 04:48:58.549692 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-16 04:48:58.845411 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-16 04:48:59.176012 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-16 04:48:59.480439 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-16 04:48:59.794762 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-16 04:49:00.095854 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-16 04:49:00.401281 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-16 04:49:00.707915 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-16 04:49:01.001624 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-16 04:49:01.329472 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-16 04:49:01.640123 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-16 04:49:02.050207 INFO::Counting total values for each feature
2024-04-16 04:49:02.117451 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-04-16 04:49:02.414472 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-04-16 04:49:02.713195 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-04-16 04:49:03.082216 INFO::Writing residuals to file output2/fits/residuals.rds
2024-04-16 04:49:03.219882 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-04-16 04:49:03.350052 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-04-16 04:49:03.361918 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-04-16 04:49:03.378131 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 59.349   1.075  68.515

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2171.943 2.891197.073