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This page was generated on 2024-03-22 11:39:11 -0400 (Fri, 22 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4646
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4426
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4407
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4283
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 1115/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.17.0  (landing page)
Lauren McIver
Snapshot Date: 2024-03-21 14:00:18 -0400 (Thu, 21 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 -0400 (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
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  

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: 1.17.0
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: 2024-03-21 21:31:35 -0400 (Thu, 21 Mar 2024)
EndedAt: 2024-03-21 21:34:44 -0400 (Thu, 21 Mar 2024)
EllapsedTime: 188.8 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) (2024-03-18 r86148)
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 98.265  2.001 100.893
* 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) (2024-03-18 r86148) -- "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"
2024-03-21 21:33:59.708593 INFO::Writing function arguments to log file
2024-03-21 21:33:59.767331 INFO::Verifying options selected are valid
2024-03-21 21:33:59.811504 INFO::Determining format of input files
2024-03-21 21:33:59.813682 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-21 21:33:59.821855 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-21 21:33:59.823815 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-03-21 21:33:59.827737 INFO::Filter data based on min abundance and min prevalence
2024-03-21 21:33:59.82926 INFO::Total samples in data: 1595
2024-03-21 21:33:59.830324 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-21 21:33:59.842296 INFO::Total filtered features: 0
2024-03-21 21:33:59.844292 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-21 21:33:59.85526 INFO::Total filtered features with variance filtering: 0
2024-03-21 21:33:59.857215 INFO::Filtered feature names from variance filtering:
2024-03-21 21:33:59.858853 INFO::Running selected normalization method: TSS
2024-03-21 21:34:01.576961 INFO::Bypass z-score application to metadata
2024-03-21 21:34:01.578974 INFO::Running selected transform method: AST
2024-03-21 21:34:01.600665 INFO::Running selected analysis method: LM
2024-03-21 21:34:02.028638 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-21 21:34:02.473245 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-21 21:34:02.613365 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-21 21:34:02.788882 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-21 21:34:02.976017 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-21 21:34:03.358599 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-21 21:34:03.482811 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-21 21:34:03.626687 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-21 21:34:03.808612 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-21 21:34:03.968277 WARNING::Fitting problem for feature 9 a warning was issued
2024-03-21 21:34:04.119517 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-21 21:34:04.287113 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-21 21:34:04.490085 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-21 21:34:04.651754 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-21 21:34:04.789205 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-21 21:34:04.995351 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-21 21:34:05.176915 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-21 21:34:05.366441 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-21 21:34:05.540972 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-21 21:34:05.727965 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-21 21:34:05.908005 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-21 21:34:06.074656 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-21 21:34:06.273468 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-21 21:34:06.445547 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-21 21:34:06.61684 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-21 21:34:06.809212 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-21 21:34:06.990529 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-21 21:34:07.165784 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-21 21:34:07.324727 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-21 21:34:07.491277 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-21 21:34:07.644314 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-21 21:34:07.833273 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-21 21:34:07.99594 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-21 21:34:08.158101 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-21 21:34:08.324853 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-21 21:34:08.507201 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-21 21:34:08.677616 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-21 21:34:08.860046 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-21 21:34:09.027133 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-21 21:34:09.199696 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-21 21:34:09.364257 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-21 21:34:09.496667 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-21 21:34:09.656292 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-21 21:34:09.815831 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-21 21:34:09.988622 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-21 21:34:10.147414 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-21 21:34:10.294872 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-21 21:34:10.471877 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-21 21:34:10.649024 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-21 21:34:10.826562 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-21 21:34:10.997597 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-21 21:34:11.182692 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-21 21:34:11.354517 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-21 21:34:11.542582 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-21 21:34:11.693718 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-21 21:34:11.855322 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-21 21:34:12.010191 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-21 21:34:12.172072 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-21 21:34:12.350015 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-21 21:34:12.527823 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-21 21:34:12.934561 WARNING::Fitting problem for feature 58 a warning was issued
2024-03-21 21:34:13.107476 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-21 21:34:13.26722 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-21 21:34:13.424438 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-21 21:34:13.593352 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-21 21:34:13.764064 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-21 21:34:13.93692 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-21 21:34:14.080308 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-21 21:34:14.238125 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-21 21:34:14.400336 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-21 21:34:14.551451 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-21 21:34:14.704111 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-21 21:34:14.866148 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-21 21:34:15.063543 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-21 21:34:15.237314 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-21 21:34:15.376876 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-21 21:34:15.518547 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-21 21:34:15.69514 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-21 21:34:15.87005 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-21 21:34:16.057042 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-21 21:34:16.232287 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-21 21:34:16.354856 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-21 21:34:16.531685 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-21 21:34:16.702684 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-21 21:34:16.881609 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-21 21:34:17.075252 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-21 21:34:17.245925 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-21 21:34:17.402413 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-21 21:34:17.518884 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-21 21:34:17.633443 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-21 21:34:17.758444 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-21 21:34:17.970741 INFO::Counting total values for each feature
2024-03-21 21:34:18.021392 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-03-21 21:34:18.149879 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-03-21 21:34:18.326124 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-03-21 21:34:18.502619 INFO::Writing residuals to file output/fits/residuals.rds
2024-03-21 21:34:18.565355 INFO::Writing fitted values to file output/fits/fitted.rds
2024-03-21 21:34:18.595999 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-03-21 21:34:18.603534 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-03-21 21:34:18.613286 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"
2024-03-21 21:34:18.634134 INFO::Writing function arguments to log file
2024-03-21 21:34:18.646587 INFO::Verifying options selected are valid
2024-03-21 21:34:18.648254 INFO::Determining format of input files
2024-03-21 21:34:18.650118 INFO::Input format is data samples as rows and metadata samples as rows
2024-03-21 21:34:18.658131 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-03-21 21:34:18.660105 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-03-21 21:34:18.662688 INFO::Filter data based on min abundance and min prevalence
2024-03-21 21:34:18.663978 INFO::Total samples in data: 1595
2024-03-21 21:34:18.665189 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-03-21 21:34:18.670084 INFO::Total filtered features: 0
2024-03-21 21:34:18.671741 INFO::Filtered feature names from abundance and prevalence filtering:
2024-03-21 21:34:18.687558 INFO::Total filtered features with variance filtering: 0
2024-03-21 21:34:18.689252 INFO::Filtered feature names from variance filtering:
2024-03-21 21:34:18.690599 INFO::Running selected normalization method: NONE
2024-03-21 21:34:18.6919 INFO::Bypass z-score application to metadata
2024-03-21 21:34:18.693163 INFO::Running selected transform method: AST
2024-03-21 21:34:18.709454 INFO::Running selected analysis method: LM
2024-03-21 21:34:18.712072 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-03-21 21:34:18.866529 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-03-21 21:34:18.995304 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-03-21 21:34:19.174357 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-03-21 21:34:19.328309 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-03-21 21:34:19.446571 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-03-21 21:34:19.855455 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-03-21 21:34:20.024943 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-03-21 21:34:20.199051 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-03-21 21:34:20.351004 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-03-21 21:34:20.526415 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-03-21 21:34:20.691271 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-03-21 21:34:20.833117 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-03-21 21:34:20.98778 WARNING::Fitting problem for feature 13 a warning was issued
2024-03-21 21:34:21.175572 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-03-21 21:34:21.340143 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-03-21 21:34:21.513808 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-03-21 21:34:21.644908 WARNING::Fitting problem for feature 16 a warning was issued
2024-03-21 21:34:21.816839 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-03-21 21:34:21.997173 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-03-21 21:34:22.178203 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-03-21 21:34:22.354727 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-03-21 21:34:22.535832 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-03-21 21:34:22.702505 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-03-21 21:34:22.852506 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-03-21 21:34:23.028707 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-03-21 21:34:23.204428 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-03-21 21:34:23.381703 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-03-21 21:34:23.541968 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-03-21 21:34:23.705296 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-03-21 21:34:23.859919 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-03-21 21:34:24.032058 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-03-21 21:34:24.183624 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-03-21 21:34:24.358568 INFO::Fitting model to feature number 32, Prevotella.copri
2024-03-21 21:34:24.554072 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-03-21 21:34:24.725661 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-03-21 21:34:24.88649 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-03-21 21:34:25.089377 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-03-21 21:34:25.240393 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-03-21 21:34:25.404366 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-03-21 21:34:25.567484 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-03-21 21:34:25.714418 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-03-21 21:34:25.871732 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-03-21 21:34:26.014789 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-03-21 21:34:26.179596 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-03-21 21:34:26.345455 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-03-21 21:34:26.494515 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-03-21 21:34:26.658346 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-03-21 21:34:26.825161 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-03-21 21:34:26.944952 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-03-21 21:34:27.104633 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-03-21 21:34:27.265147 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-03-21 21:34:27.423389 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-03-21 21:34:27.597052 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-03-21 21:34:27.783122 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-03-21 21:34:27.931268 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-03-21 21:34:28.088626 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-03-21 21:34:28.259596 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-03-21 21:34:28.419178 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-03-21 21:34:28.580658 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-03-21 21:34:28.728294 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-03-21 21:34:28.895705 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-03-21 21:34:29.004552 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-03-21 21:34:29.164476 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-03-21 21:34:29.344127 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-03-21 21:34:29.502217 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-03-21 21:34:29.674328 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-03-21 21:34:29.846932 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-03-21 21:34:30.002017 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-03-21 21:34:30.159928 WARNING::Fitting problem for feature 67 a warning was issued
2024-03-21 21:34:30.340779 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-03-21 21:34:30.485249 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-03-21 21:34:30.667299 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-03-21 21:34:30.844518 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-03-21 21:34:31.019995 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-03-21 21:34:31.077991 WARNING::Fitting problem for feature 72 a warning was issued
2024-03-21 21:34:31.229339 INFO::Fitting model to feature number 73, Dialister.invisus
2024-03-21 21:34:31.3443 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-03-21 21:34:31.490013 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-03-21 21:34:31.656993 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-03-21 21:34:31.824011 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-03-21 21:34:31.996613 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-03-21 21:34:32.174856 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-03-21 21:34:32.325456 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-03-21 21:34:32.512208 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-03-21 21:34:32.692765 INFO::Fitting model to feature number 82, Escherichia.coli
2024-03-21 21:34:32.872273 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-03-21 21:34:33.023178 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-03-21 21:34:33.202102 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-03-21 21:34:33.370189 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-03-21 21:34:33.553493 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-03-21 21:34:33.769248 INFO::Counting total values for each feature
2024-03-21 21:34:33.795519 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-03-21 21:34:33.946936 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-03-21 21:34:34.085352 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-03-21 21:34:34.281536 INFO::Writing residuals to file output2/fits/residuals.rds
2024-03-21 21:34:34.366286 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-03-21 21:34:34.446535 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-03-21 21:34:34.454805 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-03-21 21:34:34.463409 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 
 35.254   0.874  36.338 

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2 98.265 2.001100.893