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This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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: 2024-07-10 14:00 -0400 (Wed, 10 Jul 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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

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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-07-11 06:46:48 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 06:53:22 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 393.2 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.5
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 188.045  3.268 230.008
* 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
  ‘/Users/biocbuild/bbs-3.19-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/4.4-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 1.9.11
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) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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"
2024-07-11 06:51:52.808525 INFO::Writing function arguments to log file
2024-07-11 06:51:52.926009 INFO::Verifying options selected are valid
2024-07-11 06:51:53.019469 INFO::Determining format of input files
2024-07-11 06:51:53.022407 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-11 06:51:53.038841 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-11 06:51:53.042543 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-11 06:51:53.05095 INFO::Filter data based on min abundance and min prevalence
2024-07-11 06:51:53.053901 INFO::Total samples in data: 1595
2024-07-11 06:51:53.056214 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-11 06:51:53.085961 INFO::Total filtered features: 0
2024-07-11 06:51:53.090899 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-11 06:51:53.116488 INFO::Total filtered features with variance filtering: 0
2024-07-11 06:51:53.119129 INFO::Filtered feature names from variance filtering:
2024-07-11 06:51:53.121727 INFO::Running selected normalization method: TSS
2024-07-11 06:51:56.052774 INFO::Bypass z-score application to metadata
2024-07-11 06:51:56.056958 INFO::Running selected transform method: AST
2024-07-11 06:51:56.098895 INFO::Running selected analysis method: LM
2024-07-11 06:51:57.409729 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-11 06:51:58.309879 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-11 06:51:58.730709 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-11 06:51:59.149019 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-11 06:51:59.563965 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-11 06:51:59.936263 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-11 06:52:00.313773 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-11 06:52:00.706083 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-11 06:52:01.090698 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-11 06:52:01.518592 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-11 06:52:01.888289 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-11 06:52:02.273929 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-11 06:52:02.639606 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-11 06:52:02.950657 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-11 06:52:03.369528 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-11 06:52:03.74517 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-11 06:52:04.16428 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-11 06:52:04.538558 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-11 06:52:04.948316 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-11 06:52:05.337629 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-11 06:52:05.728632 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-11 06:52:06.107251 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-11 06:52:06.494618 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-11 06:52:06.877031 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-11 06:52:07.25495 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-11 06:52:07.640715 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-11 06:52:08.062111 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-11 06:52:08.420163 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-11 06:52:08.809543 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-11 06:52:09.178138 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-11 06:52:09.570494 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-11 06:52:09.938636 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-11 06:52:10.332398 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-11 06:52:10.704454 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-11 06:52:11.103304 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-11 06:52:11.471422 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-11 06:52:11.838361 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-11 06:52:12.229214 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-11 06:52:12.608212 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-11 06:52:12.989757 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-11 06:52:13.659185 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-11 06:52:14.047346 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-11 06:52:14.427772 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-11 06:52:14.821491 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-11 06:52:15.204207 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-11 06:52:15.557781 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-11 06:52:15.911721 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-11 06:52:16.294236 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-11 06:52:16.683316 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-11 06:52:17.051119 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-11 06:52:17.43469 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-11 06:52:17.789465 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-11 06:52:18.156383 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-11 06:52:18.554599 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-11 06:52:18.936156 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-11 06:52:19.301067 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-11 06:52:19.684042 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-11 06:52:20.06673 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-11 06:52:20.413608 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-11 06:52:20.813723 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-11 06:52:21.189585 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-11 06:52:21.551761 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-11 06:52:21.925198 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-11 06:52:22.301751 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-11 06:52:22.657852 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-11 06:52:23.048744 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-11 06:52:23.413359 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-11 06:52:23.780259 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-11 06:52:24.126281 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-11 06:52:24.498024 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-11 06:52:24.848663 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-11 06:52:25.204846 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-11 06:52:25.596998 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-11 06:52:25.966749 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-11 06:52:26.323547 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-11 06:52:26.704928 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-11 06:52:27.066317 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-11 06:52:27.717791 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-11 06:52:28.09566 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-11 06:52:28.484812 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-11 06:52:28.844875 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-11 06:52:29.231462 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-11 06:52:29.613929 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-11 06:52:29.990653 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-11 06:52:30.371381 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-11 06:52:30.765519 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-11 06:52:31.131171 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-11 06:52:31.486092 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-11 06:52:31.99164 INFO::Counting total values for each feature
2024-07-11 06:52:32.098511 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-11 06:52:32.439198 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-11 06:52:32.884047 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-11 06:52:33.329038 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-11 06:52:33.448831 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-11 06:52:33.51782 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-11 06:52:33.533393 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-11 06:52:33.552666 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"
2024-07-11 06:52:33.597533 INFO::Writing function arguments to log file
2024-07-11 06:52:33.655944 INFO::Verifying options selected are valid
2024-07-11 06:52:33.658719 INFO::Determining format of input files
2024-07-11 06:52:33.661874 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-11 06:52:33.676999 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-11 06:52:33.67979 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-11 06:52:33.684427 INFO::Filter data based on min abundance and min prevalence
2024-07-11 06:52:33.689755 INFO::Total samples in data: 1595
2024-07-11 06:52:33.693421 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-11 06:52:33.703544 INFO::Total filtered features: 0
2024-07-11 06:52:33.706517 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-11 06:52:33.724764 INFO::Total filtered features with variance filtering: 0
2024-07-11 06:52:33.728636 INFO::Filtered feature names from variance filtering:
2024-07-11 06:52:33.731298 INFO::Running selected normalization method: NONE
2024-07-11 06:52:33.733602 INFO::Bypass z-score application to metadata
2024-07-11 06:52:33.735788 INFO::Running selected transform method: AST
2024-07-11 06:52:33.771006 INFO::Running selected analysis method: LM
2024-07-11 06:52:33.774362 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-11 06:52:34.116618 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-11 06:52:34.461706 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-11 06:52:34.798249 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-11 06:52:35.164237 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-11 06:52:35.535102 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-11 06:52:35.930714 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-11 06:52:36.286113 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-11 06:52:36.638307 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-11 06:52:37.000363 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-11 06:52:37.349183 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-11 06:52:37.713906 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-11 06:52:38.065926 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-11 06:52:38.380969 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-11 06:52:38.788345 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-11 06:52:39.142442 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-11 06:52:39.524808 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-11 06:52:39.886245 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-11 06:52:40.258739 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-11 06:52:40.616856 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-11 06:52:40.95777 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-11 06:52:41.309097 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-11 06:52:41.666146 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-11 06:52:42.020994 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-11 06:52:42.376005 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-11 06:52:42.734463 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-11 06:52:43.080352 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-11 06:52:43.453186 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-11 06:52:43.816781 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-11 06:52:44.145925 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-11 06:52:44.473259 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-11 06:52:44.828971 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-11 06:52:45.171376 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-11 06:52:45.534325 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-11 06:52:45.885764 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-11 06:52:46.231291 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-11 06:52:46.572783 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-11 06:52:46.946029 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-11 06:52:47.293219 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-11 06:52:47.64668 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-11 06:52:48.011549 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-11 06:52:48.355157 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-11 06:52:48.705511 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-11 06:52:49.103059 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-11 06:52:49.443501 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-11 06:52:49.79388 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-11 06:52:50.146451 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-11 06:52:50.537098 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-11 06:52:50.875561 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-11 06:52:51.232077 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-11 06:52:51.581806 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-11 06:52:51.93889 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-11 06:52:52.289008 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-11 06:52:52.629851 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-11 06:52:52.978585 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-11 06:52:53.344955 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-11 06:52:53.695059 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-11 06:52:54.046193 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-11 06:52:54.405023 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-11 06:52:54.763144 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-11 06:52:55.103879 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-11 06:52:55.465169 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-11 06:52:55.805578 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-11 06:52:56.175429 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-11 06:52:56.544804 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-11 06:52:56.885456 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-11 06:52:57.213808 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-11 06:52:57.536797 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-11 06:52:57.838487 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-11 06:52:58.222925 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-11 06:52:58.570915 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-11 06:52:58.947461 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-11 06:52:59.331668 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-11 06:52:59.666849 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-11 06:52:59.789464 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-11 06:53:00.142166 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-11 06:53:00.516406 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-11 06:53:00.877239 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-11 06:53:01.259165 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-11 06:53:01.62011 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-11 06:53:01.979519 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-11 06:53:02.326676 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-11 06:53:02.685531 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-11 06:53:03.049802 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-11 06:53:03.413852 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-11 06:53:03.761963 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-11 06:53:04.096622 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-11 06:53:04.455451 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-11 06:53:04.809634 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-11 06:53:05.177055 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-11 06:53:05.625985 INFO::Counting total values for each feature
2024-07-11 06:53:05.704581 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-11 06:53:06.066223 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-11 06:53:06.420824 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-11 06:53:06.865716 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-11 06:53:07.007539 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-11 06:53:07.145053 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-11 06:53:07.157633 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-11 06:53:07.172612 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 
 63.774   1.275  77.500

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2188.045 3.268230.008