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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 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
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: 2024-06-23 14:00 -0400 (Sun, 23 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

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: 2024-06-24 06:47:53 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 06:54:33 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 399.8 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 4.4.0 (2024-04-24)
* 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 12.7.4
* 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 189.726  3.266 235.379
* 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 1.9.12
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) -- "Puppy Cup"
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"
2024-06-24 06:53:02.493513 INFO::Writing function arguments to log file
2024-06-24 06:53:02.618913 INFO::Verifying options selected are valid
2024-06-24 06:53:02.711958 INFO::Determining format of input files
2024-06-24 06:53:02.716062 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-24 06:53:02.740363 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-24 06:53:02.745075 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-24 06:53:02.753894 INFO::Filter data based on min abundance and min prevalence
2024-06-24 06:53:02.756833 INFO::Total samples in data: 1595
2024-06-24 06:53:02.760113 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-24 06:53:02.79083 INFO::Total filtered features: 0
2024-06-24 06:53:02.793663 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-24 06:53:02.816827 INFO::Total filtered features with variance filtering: 0
2024-06-24 06:53:02.819589 INFO::Filtered feature names from variance filtering:
2024-06-24 06:53:02.821913 INFO::Running selected normalization method: TSS
2024-06-24 06:53:05.765025 INFO::Bypass z-score application to metadata
2024-06-24 06:53:05.76778 INFO::Running selected transform method: AST
2024-06-24 06:53:05.813108 INFO::Running selected analysis method: LM
2024-06-24 06:53:07.139225 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-24 06:53:08.073483 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-24 06:53:08.54225 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-24 06:53:08.96494 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-24 06:53:09.36583 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-24 06:53:09.729316 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-24 06:53:10.118141 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-24 06:53:10.505602 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-24 06:53:10.89017 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-24 06:53:11.325407 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-24 06:53:11.713656 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-24 06:53:12.107933 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-24 06:53:12.473933 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-24 06:53:12.786495 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-24 06:53:13.218509 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-24 06:53:13.601908 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-24 06:53:13.993987 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-24 06:53:14.386574 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-24 06:53:14.796519 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-24 06:53:15.178334 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-24 06:53:15.563098 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-24 06:53:15.958278 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-24 06:53:16.348719 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-24 06:53:16.738138 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-24 06:53:17.100137 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-24 06:53:17.481913 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-24 06:53:17.872978 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-24 06:53:18.247829 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-24 06:53:18.639865 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-24 06:53:19.014991 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-24 06:53:19.401828 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-24 06:53:19.800706 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-24 06:53:20.234441 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-24 06:53:20.663568 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-24 06:53:21.11365 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-24 06:53:21.495035 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-24 06:53:21.876466 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-24 06:53:22.240376 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-24 06:53:22.622217 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-24 06:53:23.006043 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-24 06:53:23.372307 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-24 06:53:23.777706 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-24 06:53:24.155888 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-24 06:53:24.56248 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-24 06:53:24.942145 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-24 06:53:25.30672 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-24 06:53:25.703013 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-24 06:53:26.096059 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-24 06:53:26.807165 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-24 06:53:27.169127 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-24 06:53:27.556925 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-24 06:53:27.929155 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-24 06:53:28.310391 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-24 06:53:28.679999 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-24 06:53:29.081683 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-24 06:53:29.461525 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-24 06:53:29.850886 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-24 06:53:30.256329 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-24 06:53:30.644572 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-24 06:53:31.005563 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-24 06:53:31.368486 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-24 06:53:31.740854 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-24 06:53:32.108047 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-24 06:53:32.483853 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-24 06:53:32.847993 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-24 06:53:33.217148 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-24 06:53:33.589501 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-24 06:53:33.9911 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-24 06:53:34.338452 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-24 06:53:34.696539 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-24 06:53:35.087457 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-24 06:53:35.467451 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-24 06:53:35.871581 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-24 06:53:36.231279 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-24 06:53:36.597792 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-24 06:53:36.996288 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-24 06:53:37.394523 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-24 06:53:37.778559 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-24 06:53:38.141722 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-24 06:53:38.667567 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-24 06:53:39.056877 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-24 06:53:39.417477 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-24 06:53:39.802159 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-24 06:53:40.187226 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-24 06:53:40.55058 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-24 06:53:40.911085 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-24 06:53:41.271273 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-24 06:53:41.614483 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-24 06:53:42.134991 INFO::Counting total values for each feature
2024-06-24 06:53:42.260253 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-24 06:53:42.751806 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-24 06:53:43.147044 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-24 06:53:43.578707 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-24 06:53:43.701537 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-24 06:53:43.766028 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-24 06:53:43.780581 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-24 06:53:43.80115 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"
2024-06-24 06:53:43.836487 INFO::Writing function arguments to log file
2024-06-24 06:53:43.857079 INFO::Verifying options selected are valid
2024-06-24 06:53:43.864995 INFO::Determining format of input files
2024-06-24 06:53:43.868205 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-24 06:53:43.882289 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-24 06:53:43.886093 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-24 06:53:43.890633 INFO::Filter data based on min abundance and min prevalence
2024-06-24 06:53:43.893379 INFO::Total samples in data: 1595
2024-06-24 06:53:43.899126 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-24 06:53:43.910878 INFO::Total filtered features: 0
2024-06-24 06:53:43.914021 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-24 06:53:43.954362 INFO::Total filtered features with variance filtering: 0
2024-06-24 06:53:43.95831 INFO::Filtered feature names from variance filtering:
2024-06-24 06:53:43.96091 INFO::Running selected normalization method: NONE
2024-06-24 06:53:43.965007 INFO::Bypass z-score application to metadata
2024-06-24 06:53:43.968099 INFO::Running selected transform method: AST
2024-06-24 06:53:44.03126 INFO::Running selected analysis method: LM
2024-06-24 06:53:44.036744 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-24 06:53:44.406699 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-24 06:53:44.771374 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-24 06:53:45.131716 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-24 06:53:45.486971 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-24 06:53:45.837308 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-24 06:53:46.19853 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-24 06:53:46.547687 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-24 06:53:46.928808 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-24 06:53:47.271639 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-24 06:53:47.634028 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-24 06:53:48.151406 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-24 06:53:48.501591 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-24 06:53:48.815273 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-24 06:53:49.230491 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-24 06:53:49.589651 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-24 06:53:49.96307 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-24 06:53:50.292076 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-24 06:53:50.638203 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-24 06:53:51.014915 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-24 06:53:51.355495 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-24 06:53:51.729568 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-24 06:53:52.080379 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-24 06:53:52.413877 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-24 06:53:52.776683 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-24 06:53:53.158675 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-24 06:53:53.502408 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-24 06:53:53.875633 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-24 06:53:54.2266 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-24 06:53:54.579757 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-24 06:53:54.955888 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-24 06:53:55.303305 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-24 06:53:55.642911 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-24 06:53:56.000626 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-24 06:53:56.342149 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-24 06:53:56.698639 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-24 06:53:57.075033 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-24 06:53:57.424756 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-24 06:53:57.795593 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-24 06:53:58.142261 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-24 06:53:58.483786 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-24 06:53:58.842438 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-24 06:53:59.207402 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-24 06:53:59.598936 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-24 06:53:59.960591 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-24 06:54:00.322525 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-24 06:54:00.676554 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-24 06:54:01.064651 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-24 06:54:01.406114 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-24 06:54:01.784344 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-24 06:54:02.135138 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-24 06:54:02.49034 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-24 06:54:02.852257 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-24 06:54:03.234402 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-24 06:54:03.583099 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-24 06:54:03.927888 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-24 06:54:04.303151 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-24 06:54:04.662005 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-24 06:54:05.00965 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-24 06:54:05.372757 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-24 06:54:05.729036 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-24 06:54:06.083492 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-24 06:54:06.420909 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-24 06:54:06.762833 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-24 06:54:07.13777 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-24 06:54:07.486569 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-24 06:54:07.843907 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-24 06:54:08.201273 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-24 06:54:08.495957 WARNING::Fitting problem for feature 67 a warning was issued
2024-06-24 06:54:09.197172 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-24 06:54:09.545377 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-24 06:54:09.905347 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-24 06:54:10.271346 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-24 06:54:10.644427 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-24 06:54:10.759374 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-24 06:54:11.119343 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-24 06:54:11.475421 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-24 06:54:11.840566 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-24 06:54:12.214087 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-24 06:54:12.561084 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-24 06:54:12.902932 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-24 06:54:13.260303 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-24 06:54:13.649945 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-24 06:54:14.018114 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-24 06:54:14.383687 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-24 06:54:14.735685 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-24 06:54:15.090205 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-24 06:54:15.415734 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-24 06:54:15.752409 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-24 06:54:16.105748 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-24 06:54:16.570349 INFO::Counting total values for each feature
2024-06-24 06:54:16.677876 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-24 06:54:17.133934 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-24 06:54:17.568685 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-24 06:54:18.021676 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-24 06:54:18.207534 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-24 06:54:18.337601 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-24 06:54:18.349971 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-24 06:54:18.363254 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 
 64.275   1.268  79.121

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2189.726 3.266235.379