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This page was generated on 2024-05-04 11:39:27 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.18.0
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: 2024-05-03 22:53:39 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:56:48 -0400 (Fri, 03 May 2024)
EllapsedTime: 188.6 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 beta (2024-04-14 r86421)
* 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 ‘1.18.0’
* 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 97.608  2.202 100.777
* 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 1.9.10
Current TMB version is 1.9.11
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-14 r86421) -- "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"
2024-05-03 22:56:04.670786 INFO::Writing function arguments to log file
2024-05-03 22:56:04.731162 INFO::Verifying options selected are valid
2024-05-03 22:56:04.7782 INFO::Determining format of input files
2024-05-03 22:56:04.780459 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-03 22:56:04.788116 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-03 22:56:04.790313 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-03 22:56:04.793985 INFO::Filter data based on min abundance and min prevalence
2024-05-03 22:56:04.795542 INFO::Total samples in data: 1595
2024-05-03 22:56:04.797099 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-03 22:56:04.812563 INFO::Total filtered features: 0
2024-05-03 22:56:04.814439 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-03 22:56:04.826941 INFO::Total filtered features with variance filtering: 0
2024-05-03 22:56:04.828766 INFO::Filtered feature names from variance filtering:
2024-05-03 22:56:04.830254 INFO::Running selected normalization method: TSS
2024-05-03 22:56:06.251518 INFO::Bypass z-score application to metadata
2024-05-03 22:56:06.252789 INFO::Running selected transform method: AST
2024-05-03 22:56:06.274007 INFO::Running selected analysis method: LM
2024-05-03 22:56:06.872484 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-03 22:56:07.29207 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-03 22:56:07.507429 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-03 22:56:07.692178 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-03 22:56:07.864295 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-03 22:56:08.02646 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-03 22:56:08.206262 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-03 22:56:08.381161 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-03 22:56:08.539976 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-03 22:56:08.771999 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-03 22:56:08.89967 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-03 22:56:09.058076 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-03 22:56:09.227119 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-03 22:56:09.350437 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-03 22:56:09.526424 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-03 22:56:09.698167 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-03 22:56:09.881767 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-03 22:56:10.051378 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-03 22:56:10.217783 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-03 22:56:10.375424 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-03 22:56:10.563722 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-03 22:56:10.747968 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-03 22:56:10.932274 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-03 22:56:11.122954 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-03 22:56:11.311514 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-03 22:56:11.487353 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-03 22:56:11.673446 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-03 22:56:11.848592 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-03 22:56:12.035292 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-03 22:56:12.206183 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-03 22:56:12.379706 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-03 22:56:12.538234 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-03 22:56:12.715067 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-03 22:56:12.894359 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-03 22:56:13.055942 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-03 22:56:13.228469 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-03 22:56:13.390439 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-03 22:56:13.560239 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-03 22:56:13.741479 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-03 22:56:13.9068 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-03 22:56:14.071292 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-03 22:56:14.24937 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-03 22:56:14.644513 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-03 22:56:14.814166 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-03 22:56:14.984246 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-03 22:56:15.159793 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-03 22:56:15.335554 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-03 22:56:15.502157 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-03 22:56:15.692343 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-03 22:56:15.84631 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-03 22:56:16.019171 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-03 22:56:16.18873 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-03 22:56:16.367869 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-03 22:56:16.537272 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-03 22:56:16.727015 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-03 22:56:16.896412 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-03 22:56:17.072465 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-03 22:56:17.255682 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-03 22:56:17.435584 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-03 22:56:17.610833 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-03 22:56:17.787976 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-03 22:56:17.974311 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-03 22:56:18.158147 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-03 22:56:18.328585 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-03 22:56:18.504385 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-03 22:56:18.660486 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-03 22:56:18.824782 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-03 22:56:19.012561 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-03 22:56:19.173806 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-03 22:56:19.347428 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-03 22:56:19.546353 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-03 22:56:19.726965 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-03 22:56:19.885734 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-03 22:56:20.055685 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-03 22:56:20.225752 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-03 22:56:20.38569 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-03 22:56:20.55743 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-03 22:56:20.715814 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-03 22:56:20.878842 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-03 22:56:21.07326 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-03 22:56:21.247332 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-03 22:56:21.414576 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-03 22:56:21.590565 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-03 22:56:21.763499 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-03 22:56:21.952787 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-03 22:56:22.123916 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-03 22:56:22.301662 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-03 22:56:22.74405 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-03 22:56:22.978737 INFO::Counting total values for each feature
2024-05-03 22:56:23.022955 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-03 22:56:23.174505 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-03 22:56:23.355411 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-03 22:56:23.543431 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-03 22:56:23.605767 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-03 22:56:23.639085 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-03 22:56:23.646731 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-03 22:56:23.65501 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"
2024-05-03 22:56:23.672698 INFO::Writing function arguments to log file
2024-05-03 22:56:23.682684 INFO::Verifying options selected are valid
2024-05-03 22:56:23.684457 INFO::Determining format of input files
2024-05-03 22:56:23.686198 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-03 22:56:23.695106 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-03 22:56:23.697334 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-03 22:56:23.700098 INFO::Filter data based on min abundance and min prevalence
2024-05-03 22:56:23.701753 INFO::Total samples in data: 1595
2024-05-03 22:56:23.703205 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-03 22:56:23.709034 INFO::Total filtered features: 0
2024-05-03 22:56:23.710626 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-03 22:56:23.719359 INFO::Total filtered features with variance filtering: 0
2024-05-03 22:56:23.721271 INFO::Filtered feature names from variance filtering:
2024-05-03 22:56:23.722868 INFO::Running selected normalization method: NONE
2024-05-03 22:56:23.724443 INFO::Bypass z-score application to metadata
2024-05-03 22:56:23.726021 INFO::Running selected transform method: AST
2024-05-03 22:56:23.756603 INFO::Running selected analysis method: LM
2024-05-03 22:56:23.75907 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-03 22:56:23.93995 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-03 22:56:24.121683 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-03 22:56:24.296428 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-03 22:56:24.466905 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-03 22:56:24.635785 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-03 22:56:24.800387 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-03 22:56:24.97447 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-03 22:56:25.134934 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-03 22:56:25.32355 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-03 22:56:25.468585 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-03 22:56:25.631084 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-03 22:56:25.796787 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-03 22:56:25.937168 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-03 22:56:26.115632 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-03 22:56:26.293745 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-03 22:56:26.473487 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-03 22:56:26.627224 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-03 22:56:26.792473 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-03 22:56:26.960491 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-03 22:56:27.133891 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-03 22:56:27.306813 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-03 22:56:27.438326 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-03 22:56:27.607238 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-03 22:56:27.766948 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-03 22:56:27.920147 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-03 22:56:28.086813 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-03 22:56:28.240123 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-03 22:56:28.399576 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-03 22:56:28.548827 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-03 22:56:28.701577 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-03 22:56:28.8663 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-03 22:56:29.028341 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-03 22:56:29.194216 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-03 22:56:29.350962 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-03 22:56:29.505628 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-03 22:56:29.657951 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-03 22:56:29.816584 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-03 22:56:29.971903 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-03 22:56:30.142674 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-03 22:56:30.319099 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-03 22:56:30.480169 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-03 22:56:30.658444 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-03 22:56:30.849995 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-03 22:56:31.037642 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-03 22:56:31.218754 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-03 22:56:31.392185 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-03 22:56:31.581055 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-03 22:56:31.738505 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-03 22:56:31.910269 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-03 22:56:32.087722 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-03 22:56:32.244206 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-03 22:56:32.410536 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-03 22:56:32.57121 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-03 22:56:32.732551 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-03 22:56:32.893818 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-03 22:56:33.027264 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-03 22:56:33.181442 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-03 22:56:33.332476 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-03 22:56:33.496423 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-03 22:56:33.667558 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-03 22:56:33.82401 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-03 22:56:33.97814 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-03 22:56:34.132349 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-03 22:56:34.297874 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-03 22:56:34.448286 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-03 22:56:34.593788 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-03 22:56:34.746855 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-03 22:56:34.882996 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-03 22:56:35.053084 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-03 22:56:35.194964 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-03 22:56:35.358893 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-03 22:56:35.54631 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-03 22:56:35.707483 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-03 22:56:35.752185 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-03 22:56:35.895451 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-03 22:56:36.076927 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-03 22:56:36.239115 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-03 22:56:36.41139 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-03 22:56:36.583393 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-03 22:56:36.770737 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-03 22:56:36.939265 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-03 22:56:37.120269 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-03 22:56:37.300495 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-03 22:56:37.500865 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-03 22:56:37.676997 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-03 22:56:37.842523 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-03 22:56:38.016259 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-03 22:56:38.195051 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-03 22:56:38.376371 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-03 22:56:38.570422 INFO::Counting total values for each feature
2024-05-03 22:56:38.596764 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-03 22:56:38.723953 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-03 22:56:38.858305 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-03 22:56:39.029753 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-03 22:56:39.110687 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-03 22:56:39.190001 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-03 22:56:39.197165 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-03 22:56:39.205039 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 
 34.779   0.941  36.111 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 97.608 2.202100.777