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This page was generated on 2024-07-06 11:43 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4391
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 3833
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 1108/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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 kjohnson3

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: 2024-07-06 01:57:17 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 01:58:46 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 88.9 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: aarch64-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 Ventura 13.6.5
* 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 35.803  0.649  46.886
* 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-arm64/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: aarch64-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"
2024-07-06 01:58:23.743134 INFO::Writing function arguments to log file
2024-07-06 01:58:23.763945 INFO::Verifying options selected are valid
2024-07-06 01:58:23.788453 INFO::Determining format of input files
2024-07-06 01:58:23.789174 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 01:58:23.791531 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 01:58:23.792121 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-06 01:58:23.793116 INFO::Filter data based on min abundance and min prevalence
2024-07-06 01:58:23.793576 INFO::Total samples in data: 1595
2024-07-06 01:58:23.793884 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 01:58:23.804164 INFO::Total filtered features: 0
2024-07-06 01:58:23.804625 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 01:58:23.807934 INFO::Total filtered features with variance filtering: 0
2024-07-06 01:58:23.808341 INFO::Filtered feature names from variance filtering:
2024-07-06 01:58:23.80863 INFO::Running selected normalization method: TSS
2024-07-06 01:58:24.528373 INFO::Bypass z-score application to metadata
2024-07-06 01:58:24.529019 INFO::Running selected transform method: AST
2024-07-06 01:58:24.535264 INFO::Running selected analysis method: LM
2024-07-06 01:58:24.848036 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 01:58:25.025276 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 01:58:25.125276 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 01:58:25.20241 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 01:58:25.307304 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 01:58:25.398836 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 01:58:25.478572 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 01:58:25.573444 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 01:58:25.645912 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 01:58:25.751435 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-06 01:58:25.835501 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 01:58:25.926371 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 01:58:26.011637 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 01:58:26.080561 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 01:58:26.15454 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 01:58:26.235597 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 01:58:26.314563 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 01:58:26.382734 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 01:58:26.464122 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 01:58:26.566482 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 01:58:26.645551 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 01:58:26.722592 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 01:58:26.78719 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 01:58:26.892271 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 01:58:26.959882 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 01:58:27.053518 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 01:58:27.121324 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 01:58:27.208288 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 01:58:27.293403 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 01:58:27.369074 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 01:58:27.462423 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 01:58:27.557509 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 01:58:27.628467 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 01:58:27.71348 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 01:58:27.801498 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 01:58:27.903602 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 01:58:27.989121 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 01:58:28.073255 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 01:58:28.16371 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 01:58:28.233553 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 01:58:28.320423 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 01:58:28.411374 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 01:58:28.486043 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 01:58:28.752798 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 01:58:28.846943 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 01:58:28.930054 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 01:58:29.017651 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 01:58:29.089446 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 01:58:29.175427 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 01:58:29.256279 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 01:58:29.315462 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 01:58:29.395745 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 01:58:29.461354 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 01:58:29.542286 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 01:58:29.634908 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 01:58:29.708372 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 01:58:29.786964 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 01:58:29.8525 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 01:58:29.920646 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 01:58:30.005799 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 01:58:30.089743 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 01:58:30.153048 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 01:58:30.225815 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 01:58:30.314427 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 01:58:30.402586 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 01:58:30.472037 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 01:58:30.554698 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 01:58:30.626124 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 01:58:30.696766 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 01:58:30.793285 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 01:58:30.874624 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 01:58:30.954082 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 01:58:31.038093 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 01:58:31.108669 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 01:58:31.174369 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 01:58:31.255203 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 01:58:31.328173 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 01:58:31.402143 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 01:58:31.473196 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 01:58:31.562403 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 01:58:31.641073 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 01:58:31.749324 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 01:58:31.812075 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 01:58:31.904522 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 01:58:31.973704 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 01:58:32.073456 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 01:58:32.156732 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 01:58:32.230381 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 01:58:32.33912 INFO::Counting total values for each feature
2024-07-06 01:58:32.35288 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-06 01:58:32.4419 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-06 01:58:32.531051 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-06 01:58:32.636098 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-06 01:58:32.677211 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-06 01:58:32.71828 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-06 01:58:32.727061 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-06 01:58:32.730007 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"
2024-07-06 01:58:32.742923 INFO::Writing function arguments to log file
2024-07-06 01:58:32.749775 INFO::Verifying options selected are valid
2024-07-06 01:58:32.750236 INFO::Determining format of input files
2024-07-06 01:58:32.750685 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-06 01:58:32.752759 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-06 01:58:32.75315 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-06 01:58:32.753744 INFO::Filter data based on min abundance and min prevalence
2024-07-06 01:58:32.754047 INFO::Total samples in data: 1595
2024-07-06 01:58:32.754322 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-06 01:58:32.755921 INFO::Total filtered features: 0
2024-07-06 01:58:32.756256 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-06 01:58:32.760306 INFO::Total filtered features with variance filtering: 0
2024-07-06 01:58:32.761549 INFO::Filtered feature names from variance filtering:
2024-07-06 01:58:32.762348 INFO::Running selected normalization method: NONE
2024-07-06 01:58:32.763066 INFO::Bypass z-score application to metadata
2024-07-06 01:58:32.76375 INFO::Running selected transform method: AST
2024-07-06 01:58:32.776565 INFO::Running selected analysis method: LM
2024-07-06 01:58:32.7773 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-06 01:58:32.883783 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-06 01:58:32.982542 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-06 01:58:33.069864 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-06 01:58:33.174936 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-06 01:58:33.2482 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-06 01:58:33.338172 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-06 01:58:33.423923 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-06 01:58:33.498097 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-06 01:58:33.581276 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-06 01:58:33.664961 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-06 01:58:33.729944 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-06 01:58:33.806257 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-06 01:58:33.896953 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-06 01:58:33.96539 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-06 01:58:34.060769 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-06 01:58:34.141043 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-06 01:58:34.214726 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-06 01:58:34.303594 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-06 01:58:34.381935 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-06 01:58:34.477006 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-06 01:58:34.54697 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-06 01:58:34.640041 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-06 01:58:34.730529 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-06 01:58:34.80623 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-06 01:58:34.876487 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-06 01:58:34.962795 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-06 01:58:35.023152 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-06 01:58:35.115953 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-06 01:58:35.194063 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-06 01:58:35.264698 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-06 01:58:35.351324 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-06 01:58:35.440675 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-06 01:58:35.499898 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-06 01:58:35.594934 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-06 01:58:35.664201 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-06 01:58:35.740947 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-06 01:58:35.824261 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-06 01:58:35.896801 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-06 01:58:35.972502 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-06 01:58:36.043133 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-06 01:58:36.117895 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-06 01:58:36.397239 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-06 01:58:36.456797 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-06 01:58:36.535958 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-06 01:58:36.612422 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-06 01:58:36.688771 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-06 01:58:36.759141 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-06 01:58:36.838557 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-06 01:58:36.918659 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-06 01:58:36.988999 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-06 01:58:37.078613 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-06 01:58:37.165438 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-06 01:58:37.237151 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-06 01:58:37.30289 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-06 01:58:37.393824 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-06 01:58:37.473885 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-06 01:58:37.545795 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-06 01:58:37.615917 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-06 01:58:37.701873 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-06 01:58:37.784931 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-06 01:58:37.851333 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-06 01:58:37.922442 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-06 01:58:38.002061 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-06 01:58:38.083181 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-06 01:58:38.167186 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-06 01:58:38.241747 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-06 01:58:38.316774 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-06 01:58:38.387449 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-06 01:58:38.475791 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-06 01:58:38.564792 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-06 01:58:38.629093 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-06 01:58:38.738644 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-06 01:58:38.818692 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-06 01:58:38.838295 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-06 01:58:38.910053 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-06 01:58:38.992395 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-06 01:58:39.069669 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-06 01:58:39.150159 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-06 01:58:39.219552 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-06 01:58:39.308759 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-06 01:58:39.3857 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-06 01:58:39.475213 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-06 01:58:39.542935 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-06 01:58:39.623253 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-06 01:58:39.717936 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-06 01:58:39.794135 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-06 01:58:39.886086 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-06 01:58:39.971966 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-06 01:58:40.061259 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-06 01:58:40.162844 INFO::Counting total values for each feature
2024-07-06 01:58:40.187352 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-06 01:58:40.244314 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-06 01:58:40.319679 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-06 01:58:40.410145 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-06 01:58:40.476576 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-06 01:58:40.536104 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-06 01:58:40.545289 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-06 01:58:40.553115 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 
 13.426   0.284  17.429

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin235.803 0.64946.886