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This page was generated on 2024-03-04 11:39:26 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1115/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.17.0  (landing page)
Lauren McIver
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: a8d86b0
git_last_commit_date: 2023-10-24 11:15:22 -0500 (Tue, 24 Oct 2023)
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
merida1macOS 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  

CHECK results for Maaslin2 on merida1


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

raw results

Summary

Package: Maaslin2
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2024-03-02 06:05:36 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 06:12:08 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 392.7 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘1.17.0’
* 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 R 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 175.989  3.658 234.597
* 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
** 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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"
2024-03-02 06:10:39.02254 INFO::Writing function arguments to log file
2024-03-02 06:10:39.135635 INFO::Verifying options selected are valid
2024-03-02 06:10:39.220984 INFO::Determining format of input files
2024-03-02 06:10:39.224249 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-02 06:10:39.246554 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-02 06:10:39.254181 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-03-02 06:10:39.260337 INFO::Filter data based on min abundance and min prevalence
2024-03-02 06:10:39.266833 INFO::Total samples in data: 1595
2024-03-02 06:10:39.269335 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-02 06:10:39.29456 INFO::Total filtered features: 0
2024-03-02 06:10:39.29743 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-02 06:10:39.321449 INFO::Total filtered features with variance filtering: 0
2024-03-02 06:10:39.328163 INFO::Filtered feature names from variance filtering:
2024-03-02 06:10:39.330472 INFO::Running selected normalization method: TSS
2024-03-02 06:10:42.515511 INFO::Bypass z-score application to metadata
2024-03-02 06:10:42.518002 INFO::Running selected transform method: AST
2024-03-02 06:10:42.56052 INFO::Running selected analysis method: LM
2024-03-02 06:10:43.57892 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-02 06:10:44.526091 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-02 06:10:44.911097 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-02 06:10:45.318357 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-02 06:10:45.713957 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-02 06:10:46.100995 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-02 06:10:46.467721 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-02 06:10:46.892058 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-02 06:10:47.276961 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-02 06:10:47.569786 WARNING::Fitting problem for feature 9 a warning was issued
2024-03-02 06:10:47.979148 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-02 06:10:48.352428 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-02 06:10:48.736337 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-02 06:10:49.109446 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-02 06:10:49.432811 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-02 06:10:49.85683 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-02 06:10:50.245604 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-02 06:10:50.62666 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-02 06:10:50.998755 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-02 06:10:51.390409 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-02 06:10:51.782507 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-02 06:10:52.137224 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-02 06:10:52.518493 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-02 06:10:52.899037 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-02 06:10:53.275829 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-02 06:10:53.673824 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-02 06:10:54.055429 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-02 06:10:54.427023 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-02 06:10:54.814275 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-02 06:10:55.205221 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-02 06:10:55.590556 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-02 06:10:55.969007 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-02 06:10:56.321886 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-02 06:10:56.714256 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-02 06:10:57.087222 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-02 06:10:57.472901 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-02 06:10:57.825191 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-02 06:10:58.197451 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-02 06:10:58.552658 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-02 06:10:58.931319 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-02 06:10:59.28517 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-02 06:10:59.650664 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-02 06:11:00.038479 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-02 06:11:00.742182 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-02 06:11:01.108746 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-02 06:11:01.468056 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-02 06:11:01.834626 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-02 06:11:02.196807 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-02 06:11:02.565559 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-02 06:11:02.960042 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-02 06:11:03.617819 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-02 06:11:04.001105 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-02 06:11:04.362269 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-02 06:11:04.734935 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-02 06:11:05.094359 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-02 06:11:05.484901 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-02 06:11:05.864955 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-02 06:11:06.23066 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-02 06:11:06.612633 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-02 06:11:06.979626 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-02 06:11:07.280297 WARNING::Fitting problem for feature 58 a warning was issued
2024-03-02 06:11:07.659778 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-02 06:11:08.026395 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-02 06:11:08.438641 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-02 06:11:08.824891 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-02 06:11:09.20606 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-02 06:11:09.561976 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-02 06:11:09.905071 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-02 06:11:10.265858 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-02 06:11:10.638546 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-02 06:11:10.922899 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-02 06:11:11.285724 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-02 06:11:11.651765 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-02 06:11:12.026732 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-02 06:11:12.388417 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-02 06:11:12.749707 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-02 06:11:13.113886 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-02 06:11:13.46534 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-02 06:11:13.830061 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-02 06:11:14.200595 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-02 06:11:14.582141 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-02 06:11:14.948534 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-02 06:11:15.329585 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-02 06:11:15.730782 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-02 06:11:16.095355 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-02 06:11:16.492319 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-02 06:11:16.878524 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-02 06:11:17.230856 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-02 06:11:17.593074 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-02 06:11:17.970494 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-02 06:11:18.335434 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-02 06:11:18.844231 INFO::Counting total values for each feature
2024-03-02 06:11:18.97509 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-03-02 06:11:19.290319 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-03-02 06:11:19.6843 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-03-02 06:11:20.109619 INFO::Writing residuals to file output/fits/residuals.rds
2024-03-02 06:11:20.218599 INFO::Writing fitted values to file output/fits/fitted.rds
2024-03-02 06:11:20.281372 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-03-02 06:11:20.293938 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-03-02 06:11:20.313716 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"
2024-03-02 06:11:20.352439 INFO::Writing function arguments to log file
2024-03-02 06:11:20.369746 INFO::Verifying options selected are valid
2024-03-02 06:11:20.372105 INFO::Determining format of input files
2024-03-02 06:11:20.378566 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-02 06:11:20.393587 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-02 06:11:20.396286 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-03-02 06:11:20.402862 INFO::Filter data based on min abundance and min prevalence
2024-03-02 06:11:20.405449 INFO::Total samples in data: 1595
2024-03-02 06:11:20.40781 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-02 06:11:20.417251 INFO::Total filtered features: 0
2024-03-02 06:11:20.419829 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-02 06:11:20.443616 INFO::Total filtered features with variance filtering: 0
2024-03-02 06:11:20.446171 INFO::Filtered feature names from variance filtering:
2024-03-02 06:11:20.448268 INFO::Running selected normalization method: NONE
2024-03-02 06:11:20.453657 INFO::Bypass z-score application to metadata
2024-03-02 06:11:20.456206 INFO::Running selected transform method: AST
2024-03-02 06:11:20.508467 INFO::Running selected analysis method: LM
2024-03-02 06:11:20.513024 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-02 06:11:20.860481 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-02 06:11:21.229566 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-02 06:11:21.549748 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-02 06:11:21.931529 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-02 06:11:22.279912 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-02 06:11:22.751507 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-02 06:11:23.12164 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-02 06:11:23.559575 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-02 06:11:23.945041 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-02 06:11:24.331218 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-02 06:11:24.69752 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-02 06:11:25.059788 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-02 06:11:25.338159 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-02 06:11:25.683995 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-02 06:11:26.036097 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-02 06:11:26.383108 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-02 06:11:26.65813 WARNING::Fitting problem for feature 16 a warning was issued
2024-03-02 06:11:27.025489 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-02 06:11:27.376325 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-02 06:11:27.705777 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-02 06:11:28.328009 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-02 06:11:28.679133 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-02 06:11:29.054425 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-02 06:11:29.401868 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-02 06:11:29.736882 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-02 06:11:30.077133 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-02 06:11:30.435122 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-02 06:11:30.799512 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-02 06:11:31.158704 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-02 06:11:31.496431 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-02 06:11:31.836591 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-02 06:11:32.190238 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-02 06:11:32.529921 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-02 06:11:32.879913 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-02 06:11:33.227063 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-02 06:11:33.56425 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-02 06:11:33.910147 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-02 06:11:34.271706 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-02 06:11:34.625342 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-02 06:11:34.977379 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-02 06:11:35.313954 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-02 06:11:35.667691 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-02 06:11:36.01301 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-02 06:11:36.35013 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-02 06:11:36.725881 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-02 06:11:37.080952 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-02 06:11:37.42527 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-02 06:11:37.791391 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-02 06:11:38.13062 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-02 06:11:38.481863 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-02 06:11:38.851281 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-02 06:11:39.201854 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-02 06:11:39.560616 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-02 06:11:39.890866 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-02 06:11:40.222681 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-02 06:11:40.544649 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-02 06:11:40.879346 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-02 06:11:41.232997 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-02 06:11:41.57157 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-02 06:11:41.885391 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-02 06:11:42.248617 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-02 06:11:42.593786 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-02 06:11:42.899038 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-02 06:11:43.221941 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-02 06:11:43.583102 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-02 06:11:43.926957 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-02 06:11:44.283533 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-02 06:11:44.633294 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-02 06:11:44.920257 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-02 06:11:45.290894 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-02 06:11:45.679314 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-02 06:11:46.044484 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-02 06:11:46.422877 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-02 06:11:46.801417 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-02 06:11:46.920475 WARNING::Fitting problem for feature 72 a warning was issued
2024-03-02 06:11:47.266294 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-02 06:11:47.613879 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-02 06:11:47.978253 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-02 06:11:48.326834 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-02 06:11:48.701479 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-02 06:11:49.048305 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-02 06:11:49.397045 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-02 06:11:49.764315 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-02 06:11:50.079326 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-02 06:11:50.45877 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-02 06:11:50.810932 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-02 06:11:51.159771 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-02 06:11:51.518277 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-02 06:11:51.845754 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-02 06:11:52.196888 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-02 06:11:52.664616 INFO::Counting total values for each feature
2024-03-02 06:11:52.742026 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-03-02 06:11:53.052954 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-03-02 06:11:53.37302 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-03-02 06:11:53.780179 INFO::Writing residuals to file output2/fits/residuals.rds
2024-03-02 06:11:53.942126 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-03-02 06:11:54.086178 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-03-02 06:11:54.100663 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-03-02 06:11:54.120329 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 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 62.262   1.280  78.230

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2175.989 3.658234.597