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This page was generated on 2024-09-17 11:40 -0400 (Tue, 17 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4445
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4450
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4483
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4430
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4428
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 1118/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-09-16 14:00 -0400 (Mon, 16 Sep 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on lconway

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Maaslin2
Version: 1.19.0
Command: /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_1.19.0.tar.gz
StartedAt: 2024-09-16 21:34:27 -0400 (Mon, 16 Sep 2024)
EndedAt: 2024-09-16 21:37:32 -0400 (Mon, 16 Sep 2024)
EllapsedTime: 185.9 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.19.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 98.181  1.717 100.545
* 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-3.20-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 1.9.15
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"
2024-09-16 21:36:49.077386 INFO::Writing function arguments to log file
2024-09-16 21:36:49.129574 INFO::Verifying options selected are valid
2024-09-16 21:36:49.173112 INFO::Determining format of input files
2024-09-16 21:36:49.17488 INFO::Input format is data samples as rows and metadata samples as rows
2024-09-16 21:36:49.181681 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-09-16 21:36:49.184083 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-09-16 21:36:49.188327 INFO::Filter data based on min abundance and min prevalence
2024-09-16 21:36:49.19005 INFO::Total samples in data: 1595
2024-09-16 21:36:49.200043 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-09-16 21:36:49.205442 INFO::Total filtered features: 0
2024-09-16 21:36:49.206936 INFO::Filtered feature names from abundance and prevalence filtering:
2024-09-16 21:36:49.217358 INFO::Total filtered features with variance filtering: 0
2024-09-16 21:36:49.218822 INFO::Filtered feature names from variance filtering:
2024-09-16 21:36:49.220021 INFO::Running selected normalization method: TSS
2024-09-16 21:36:50.723524 INFO::Bypass z-score application to metadata
2024-09-16 21:36:50.725261 INFO::Running selected transform method: AST
2024-09-16 21:36:50.745759 INFO::Running selected analysis method: LM
2024-09-16 21:36:51.165545 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-09-16 21:36:51.588188 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-09-16 21:36:51.795317 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-09-16 21:36:51.967033 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-09-16 21:36:52.144278 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-09-16 21:36:52.315625 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-09-16 21:36:52.489792 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-09-16 21:36:52.667462 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-09-16 21:36:52.873521 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-09-16 21:36:53.05321 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-09-16 21:36:53.241577 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-09-16 21:36:53.420024 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-09-16 21:36:53.599314 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-09-16 21:36:53.74382 WARNING::Fitting problem for feature 13 a warning was issued
2024-09-16 21:36:53.947402 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-09-16 21:36:54.125256 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-09-16 21:36:54.321173 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-09-16 21:36:54.494857 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-09-16 21:36:54.691841 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-09-16 21:36:54.871573 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-09-16 21:36:55.063458 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-09-16 21:36:55.252741 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-09-16 21:36:55.437008 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-09-16 21:36:55.633207 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-09-16 21:36:55.815688 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-09-16 21:36:56.011775 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-09-16 21:36:56.201313 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-09-16 21:36:56.399001 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-09-16 21:36:56.576401 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-09-16 21:36:56.760524 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-09-16 21:36:56.945281 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-09-16 21:36:57.123519 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-09-16 21:36:57.302059 INFO::Fitting model to feature number 32, Prevotella.copri
2024-09-16 21:36:57.490689 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-09-16 21:36:57.674554 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-09-16 21:36:57.863193 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-09-16 21:36:58.032323 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-09-16 21:36:58.425105 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-09-16 21:36:58.596485 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-09-16 21:36:58.760931 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-09-16 21:36:58.932919 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-09-16 21:36:59.106291 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-09-16 21:36:59.276039 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-09-16 21:36:59.694545 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-09-16 21:36:59.847491 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-09-16 21:37:00.011708 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-09-16 21:37:00.186165 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-09-16 21:37:00.360748 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-09-16 21:37:00.538216 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-09-16 21:37:00.7011 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-09-16 21:37:00.87711 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-09-16 21:37:01.05315 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-09-16 21:37:01.213814 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-09-16 21:37:01.401624 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-09-16 21:37:01.589174 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-09-16 21:37:01.759239 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-09-16 21:37:01.941259 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-09-16 21:37:02.120158 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-09-16 21:37:02.285209 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-09-16 21:37:02.479557 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-09-16 21:37:02.668287 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-09-16 21:37:02.84867 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-09-16 21:37:03.034594 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-09-16 21:37:03.227044 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-09-16 21:37:03.397011 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-09-16 21:37:03.571007 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-09-16 21:37:03.744234 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-09-16 21:37:03.91491 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-09-16 21:37:04.092677 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-09-16 21:37:04.266199 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-09-16 21:37:04.439852 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-09-16 21:37:04.597247 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-09-16 21:37:04.777945 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-09-16 21:37:04.95043 INFO::Fitting model to feature number 73, Dialister.invisus
2024-09-16 21:37:05.112857 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-09-16 21:37:05.279875 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-09-16 21:37:05.454272 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-09-16 21:37:05.649591 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-09-16 21:37:05.817161 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-09-16 21:37:05.995128 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-09-16 21:37:06.194076 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-09-16 21:37:06.363568 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-09-16 21:37:06.534506 INFO::Fitting model to feature number 82, Escherichia.coli
2024-09-16 21:37:06.742634 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-09-16 21:37:06.915329 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-09-16 21:37:07.07077 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-09-16 21:37:07.225912 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-09-16 21:37:07.39767 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-09-16 21:37:07.62911 INFO::Counting total values for each feature
2024-09-16 21:37:07.666666 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-09-16 21:37:07.810048 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-09-16 21:37:07.991103 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-09-16 21:37:08.158262 INFO::Writing residuals to file output/fits/residuals.rds
2024-09-16 21:37:08.211608 INFO::Writing fitted values to file output/fits/fitted.rds
2024-09-16 21:37:08.241366 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-09-16 21:37:08.248978 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-09-16 21:37:08.267507 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"
2024-09-16 21:37:08.287195 INFO::Writing function arguments to log file
2024-09-16 21:37:08.297826 INFO::Verifying options selected are valid
2024-09-16 21:37:08.299598 INFO::Determining format of input files
2024-09-16 21:37:08.301485 INFO::Input format is data samples as rows and metadata samples as rows
2024-09-16 21:37:08.307999 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-09-16 21:37:08.310088 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-09-16 21:37:08.312725 INFO::Filter data based on min abundance and min prevalence
2024-09-16 21:37:08.314333 INFO::Total samples in data: 1595
2024-09-16 21:37:08.315848 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-09-16 21:37:08.321436 INFO::Total filtered features: 0
2024-09-16 21:37:08.322908 INFO::Filtered feature names from abundance and prevalence filtering:
2024-09-16 21:37:08.33263 INFO::Total filtered features with variance filtering: 0
2024-09-16 21:37:08.334412 INFO::Filtered feature names from variance filtering:
2024-09-16 21:37:08.335602 INFO::Running selected normalization method: NONE
2024-09-16 21:37:08.337028 INFO::Bypass z-score application to metadata
2024-09-16 21:37:08.3396 INFO::Running selected transform method: AST
2024-09-16 21:37:08.357077 INFO::Running selected analysis method: LM
2024-09-16 21:37:08.359373 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-09-16 21:37:08.5238 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-09-16 21:37:08.692827 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-09-16 21:37:08.858825 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-09-16 21:37:09.028957 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-09-16 21:37:09.204418 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-09-16 21:37:09.37527 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-09-16 21:37:09.552926 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-09-16 21:37:09.714222 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-09-16 21:37:09.891779 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-09-16 21:37:10.052907 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-09-16 21:37:10.213292 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-09-16 21:37:10.374346 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-09-16 21:37:10.542174 WARNING::Fitting problem for feature 13 a warning was issued
2024-09-16 21:37:10.733478 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-09-16 21:37:10.904681 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-09-16 21:37:11.080753 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-09-16 21:37:11.239518 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-09-16 21:37:11.405485 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-09-16 21:37:11.580879 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-09-16 21:37:11.746028 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-09-16 21:37:11.9067 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-09-16 21:37:12.080615 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-09-16 21:37:12.243122 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-09-16 21:37:12.400262 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-09-16 21:37:12.574174 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-09-16 21:37:12.735034 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-09-16 21:37:12.88916 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-09-16 21:37:13.065234 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-09-16 21:37:13.217644 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-09-16 21:37:13.38355 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-09-16 21:37:13.554158 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-09-16 21:37:13.707347 INFO::Fitting model to feature number 32, Prevotella.copri
2024-09-16 21:37:13.882855 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-09-16 21:37:14.022875 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-09-16 21:37:14.166295 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-09-16 21:37:14.322918 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-09-16 21:37:14.477146 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-09-16 21:37:14.638029 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-09-16 21:37:14.818118 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-09-16 21:37:14.984823 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-09-16 21:37:15.160517 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-09-16 21:37:15.343132 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-09-16 21:37:15.503448 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-09-16 21:37:15.673131 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-09-16 21:37:15.836487 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-09-16 21:37:16.014106 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-09-16 21:37:16.1716 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-09-16 21:37:16.337961 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-09-16 21:37:16.496011 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-09-16 21:37:16.664433 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-09-16 21:37:16.806314 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-09-16 21:37:16.968267 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-09-16 21:37:17.115172 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-09-16 21:37:17.280417 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-09-16 21:37:17.439455 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-09-16 21:37:17.587219 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-09-16 21:37:17.759126 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-09-16 21:37:17.913451 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-09-16 21:37:18.078443 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-09-16 21:37:18.269362 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-09-16 21:37:18.417091 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-09-16 21:37:18.573346 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-09-16 21:37:18.745408 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-09-16 21:37:18.900678 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-09-16 21:37:19.075159 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-09-16 21:37:19.223025 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-09-16 21:37:19.380299 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-09-16 21:37:19.532325 WARNING::Fitting problem for feature 67 a warning was issued
2024-09-16 21:37:19.70007 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-09-16 21:37:19.853906 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-09-16 21:37:20.022568 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-09-16 21:37:20.207948 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-09-16 21:37:20.369958 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-09-16 21:37:20.433032 WARNING::Fitting problem for feature 72 a warning was issued
2024-09-16 21:37:20.628522 INFO::Fitting model to feature number 73, Dialister.invisus
2024-09-16 21:37:20.799407 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-09-16 21:37:20.976885 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-09-16 21:37:21.149341 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-09-16 21:37:21.313714 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-09-16 21:37:21.496512 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-09-16 21:37:21.673439 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-09-16 21:37:21.863268 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-09-16 21:37:22.018975 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-09-16 21:37:22.171437 INFO::Fitting model to feature number 82, Escherichia.coli
2024-09-16 21:37:22.348257 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-09-16 21:37:22.511759 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-09-16 21:37:22.69525 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-09-16 21:37:22.860934 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-09-16 21:37:23.032749 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-09-16 21:37:23.243549 INFO::Counting total values for each feature
2024-09-16 21:37:23.273116 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-09-16 21:37:23.408701 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-09-16 21:37:23.546175 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-09-16 21:37:23.728755 INFO::Writing residuals to file output2/fits/residuals.rds
2024-09-16 21:37:23.80384 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-09-16 21:37:23.876308 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-09-16 21:37:23.884869 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-09-16 21:37:23.892447 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 
 35.383   0.717  36.291

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 98.181 1.717100.545