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This page was generated on 2024-06-26 11:39 -0400 (Wed, 26 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4691
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4405
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4355
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: 2024-06-25 14:00 -0400 (Tue, 25 Jun 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
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

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: 2024-06-25 21:55:12 -0400 (Tue, 25 Jun 2024)
EndedAt: 2024-06-25 21:56:10 -0400 (Tue, 25 Jun 2024)
EllapsedTime: 57.6 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 29.382  0.544  29.983
* 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 1.9.12
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 4.4.1 RC (2024-06-06 r86719) -- "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"
2024-06-25 21:55:56.332802 INFO::Writing function arguments to log file
2024-06-25 21:55:56.348882 INFO::Verifying options selected are valid
2024-06-25 21:55:56.362846 INFO::Determining format of input files
2024-06-25 21:55:56.363445 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-25 21:55:56.365468 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-25 21:55:56.365939 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-06-25 21:55:56.366766 INFO::Filter data based on min abundance and min prevalence
2024-06-25 21:55:56.367064 INFO::Total samples in data: 1595
2024-06-25 21:55:56.367344 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-25 21:55:56.372104 INFO::Total filtered features: 0
2024-06-25 21:55:56.372483 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-25 21:55:56.375571 INFO::Total filtered features with variance filtering: 0
2024-06-25 21:55:56.375898 INFO::Filtered feature names from variance filtering:
2024-06-25 21:55:56.37618 INFO::Running selected normalization method: TSS
2024-06-25 21:55:56.819491 INFO::Bypass z-score application to metadata
2024-06-25 21:55:56.820069 INFO::Running selected transform method: AST
2024-06-25 21:55:56.826667 INFO::Running selected analysis method: LM
2024-06-25 21:55:57.038206 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-25 21:55:57.166533 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-25 21:55:57.22603 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-25 21:55:57.277251 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-25 21:55:57.335236 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-25 21:55:57.387436 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-25 21:55:57.44028 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-25 21:55:57.494517 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-25 21:55:57.544582 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-25 21:55:57.599454 WARNING::Fitting problem for feature 9 a warning was issued
2024-06-25 21:55:57.649575 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-25 21:55:57.700762 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-25 21:55:57.748742 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-25 21:55:57.80254 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-25 21:55:57.852383 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-25 21:55:57.904777 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-25 21:55:57.954298 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-25 21:55:58.007927 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-25 21:55:58.062649 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-25 21:55:58.119457 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-25 21:55:58.169401 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-25 21:55:58.234778 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-25 21:55:58.287605 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-25 21:55:58.441426 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-25 21:55:58.493305 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-25 21:55:58.549691 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-25 21:55:58.608501 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-25 21:55:58.657188 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-25 21:55:58.707195 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-25 21:55:58.75579 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-25 21:55:58.807414 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-25 21:55:58.851657 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-25 21:55:58.90038 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-25 21:55:59.053568 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-25 21:55:59.102509 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-25 21:55:59.150278 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-25 21:55:59.201131 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-25 21:55:59.251155 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-25 21:55:59.297698 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-25 21:55:59.342474 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-25 21:55:59.393934 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-25 21:55:59.444629 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-25 21:55:59.491728 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-25 21:55:59.548778 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-25 21:55:59.598142 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-25 21:55:59.647779 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-25 21:55:59.70446 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-25 21:55:59.752647 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-25 21:55:59.806367 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-25 21:55:59.86197 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-25 21:55:59.914226 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-25 21:55:59.963903 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-25 21:56:00.016556 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-25 21:56:00.067265 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-25 21:56:00.11929 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-25 21:56:00.167677 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-25 21:56:00.216325 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-25 21:56:00.272533 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-25 21:56:00.317467 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-25 21:56:00.36827 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-25 21:56:00.417602 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-25 21:56:00.462521 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-25 21:56:00.51292 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-25 21:56:00.564378 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-25 21:56:00.61357 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-25 21:56:00.660703 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-25 21:56:00.705425 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-25 21:56:00.757022 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-25 21:56:00.8032 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-25 21:56:00.858354 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-25 21:56:00.912719 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-25 21:56:00.970957 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-25 21:56:01.020198 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-25 21:56:01.069766 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-25 21:56:01.230596 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-25 21:56:01.280718 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-25 21:56:01.330636 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-25 21:56:01.387956 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-25 21:56:01.44696 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-25 21:56:01.501313 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-25 21:56:01.55507 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-25 21:56:01.605678 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-25 21:56:01.663656 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-25 21:56:01.715564 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-25 21:56:01.764599 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-25 21:56:01.815929 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-25 21:56:01.873912 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-25 21:56:01.928388 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-25 21:56:01.995086 INFO::Counting total values for each feature
2024-06-25 21:56:02.007488 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-06-25 21:56:02.055642 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-06-25 21:56:02.112579 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-06-25 21:56:02.16918 INFO::Writing residuals to file output/fits/residuals.rds
2024-06-25 21:56:02.196079 INFO::Writing fitted values to file output/fits/fitted.rds
2024-06-25 21:56:02.210221 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-06-25 21:56:02.213129 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-06-25 21:56:02.215853 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"
2024-06-25 21:56:02.220831 INFO::Writing function arguments to log file
2024-06-25 21:56:02.222734 INFO::Verifying options selected are valid
2024-06-25 21:56:02.22303 INFO::Determining format of input files
2024-06-25 21:56:02.227125 INFO::Input format is data samples as rows and metadata samples as rows
2024-06-25 21:56:02.229097 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-06-25 21:56:02.229436 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-06-25 21:56:02.229958 INFO::Filter data based on min abundance and min prevalence
2024-06-25 21:56:02.230205 INFO::Total samples in data: 1595
2024-06-25 21:56:02.230441 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-06-25 21:56:02.231763 INFO::Total filtered features: 0
2024-06-25 21:56:02.232041 INFO::Filtered feature names from abundance and prevalence filtering:
2024-06-25 21:56:02.234497 INFO::Total filtered features with variance filtering: 0
2024-06-25 21:56:02.234776 INFO::Filtered feature names from variance filtering:
2024-06-25 21:56:02.235013 INFO::Running selected normalization method: NONE
2024-06-25 21:56:02.235255 INFO::Bypass z-score application to metadata
2024-06-25 21:56:02.23549 INFO::Running selected transform method: AST
2024-06-25 21:56:02.240606 INFO::Running selected analysis method: LM
2024-06-25 21:56:02.241046 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-06-25 21:56:02.287004 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-06-25 21:56:02.333114 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-06-25 21:56:02.380786 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-06-25 21:56:02.430335 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-06-25 21:56:02.478962 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-06-25 21:56:02.530004 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-06-25 21:56:02.583823 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-06-25 21:56:02.633429 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-06-25 21:56:02.682088 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-06-25 21:56:02.733088 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-06-25 21:56:02.779863 WARNING::Fitting problem for feature 11 a warning was issued
2024-06-25 21:56:02.836029 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-06-25 21:56:02.884566 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-06-25 21:56:02.927146 WARNING::Fitting problem for feature 13 a warning was issued
2024-06-25 21:56:02.986854 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-06-25 21:56:03.035702 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-06-25 21:56:03.08611 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-06-25 21:56:03.134746 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-06-25 21:56:03.190692 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-06-25 21:56:03.240788 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-06-25 21:56:03.288407 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-06-25 21:56:03.337856 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-06-25 21:56:03.391585 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-06-25 21:56:03.441858 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-06-25 21:56:03.490576 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-06-25 21:56:03.547607 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-06-25 21:56:03.599143 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-06-25 21:56:03.648878 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-06-25 21:56:03.700569 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-06-25 21:56:03.75151 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-06-25 21:56:03.798073 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-06-25 21:56:03.846638 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-06-25 21:56:03.899401 INFO::Fitting model to feature number 32, Prevotella.copri
2024-06-25 21:56:03.95002 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-06-25 21:56:03.998908 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-06-25 21:56:04.051445 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-06-25 21:56:04.102888 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-06-25 21:56:04.152988 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-06-25 21:56:04.207303 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-06-25 21:56:04.257577 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-06-25 21:56:04.305253 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-06-25 21:56:04.358124 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-06-25 21:56:04.407371 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-06-25 21:56:04.458725 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-06-25 21:56:04.634285 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-06-25 21:56:04.685694 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-06-25 21:56:04.736106 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-06-25 21:56:04.789416 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-06-25 21:56:04.844486 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-06-25 21:56:04.897634 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-06-25 21:56:04.94642 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-06-25 21:56:04.992223 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-06-25 21:56:05.04647 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-06-25 21:56:05.090748 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-06-25 21:56:05.136469 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-06-25 21:56:05.18498 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-06-25 21:56:05.240723 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-06-25 21:56:05.292622 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-06-25 21:56:05.342407 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-06-25 21:56:05.390764 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-06-25 21:56:05.445261 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-06-25 21:56:05.492071 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-06-25 21:56:05.541591 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-06-25 21:56:05.591129 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-06-25 21:56:05.64191 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-06-25 21:56:05.704358 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-06-25 21:56:05.753169 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-06-25 21:56:05.805049 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-06-25 21:56:05.861456 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-06-25 21:56:05.913138 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-06-25 21:56:05.963971 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-06-25 21:56:06.016751 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-06-25 21:56:06.066348 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-06-25 21:56:06.084863 WARNING::Fitting problem for feature 72 a warning was issued
2024-06-25 21:56:06.137783 INFO::Fitting model to feature number 73, Dialister.invisus
2024-06-25 21:56:06.186825 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-06-25 21:56:06.236637 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-06-25 21:56:06.286281 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-06-25 21:56:06.341093 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-06-25 21:56:06.389974 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-06-25 21:56:06.440236 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-06-25 21:56:06.492394 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-06-25 21:56:06.548542 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-06-25 21:56:06.604602 INFO::Fitting model to feature number 82, Escherichia.coli
2024-06-25 21:56:06.653005 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-06-25 21:56:06.701441 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-06-25 21:56:06.753279 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-06-25 21:56:06.803214 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-06-25 21:56:06.855066 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-06-25 21:56:06.919189 INFO::Counting total values for each feature
2024-06-25 21:56:06.928485 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-06-25 21:56:06.975377 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-06-25 21:56:07.022602 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-06-25 21:56:07.077529 INFO::Writing residuals to file output2/fits/residuals.rds
2024-06-25 21:56:07.113672 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-06-25 21:56:07.1481 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-06-25 21:56:07.151145 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-06-25 21:56:07.153399 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 
 11.065   0.218  11.280

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin229.382 0.54429.983