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This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
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 1122/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'metagenomeSeq' which is not available

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: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2024-11-27 23:22:25 -0500 (Wed, 27 Nov 2024)
EndedAt: 2024-11-27 23:28:06 -0500 (Wed, 27 Nov 2024)
EllapsedTime: 340.8 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 62.231  1.085  63.577
* 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-3.21-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/4.5-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) (2024-11-20 r87352) -- "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"
2024-11-27 23:27:40.115768 INFO::Writing function arguments to log file
2024-11-27 23:27:40.151378 INFO::Verifying options selected are valid
2024-11-27 23:27:40.181582 INFO::Determining format of input files
2024-11-27 23:27:40.183048 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-27 23:27:40.188061 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-27 23:27:40.189266 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-11-27 23:27:40.191299 INFO::Filter data based on min abundance and min prevalence
2024-11-27 23:27:40.19208 INFO::Total samples in data: 1595
2024-11-27 23:27:40.192833 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-27 23:27:40.202202 INFO::Total filtered features: 0
2024-11-27 23:27:40.203235 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-27 23:27:40.209614 INFO::Total filtered features with variance filtering: 0
2024-11-27 23:27:40.210623 INFO::Filtered feature names from variance filtering:
2024-11-27 23:27:40.211467 INFO::Running selected normalization method: TSS
2024-11-27 23:27:41.069812 INFO::Bypass z-score application to metadata
2024-11-27 23:27:41.070933 INFO::Running selected transform method: AST
2024-11-27 23:27:41.084457 INFO::Running selected analysis method: LM
2024-11-27 23:27:41.478413 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-27 23:27:41.747806 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-27 23:27:41.86661 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-27 23:27:41.972689 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-27 23:27:42.084771 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-27 23:27:42.18506 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-27 23:27:42.29006 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-27 23:27:42.396344 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-27 23:27:42.496673 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-27 23:27:42.594191 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-27 23:27:42.685361 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-27 23:27:42.812993 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-27 23:27:42.903119 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-27 23:27:42.989719 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-27 23:27:43.09452 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-27 23:27:43.199351 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-27 23:27:43.296221 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-27 23:27:43.401741 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-27 23:27:43.506314 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-27 23:27:43.614753 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-27 23:27:43.708071 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-27 23:27:43.811074 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-27 23:27:43.909171 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-27 23:27:44.009218 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-27 23:27:44.108746 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-27 23:27:44.20625 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-27 23:27:44.308491 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-27 23:27:44.408382 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-27 23:27:44.533718 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-27 23:27:44.631759 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-27 23:27:44.731918 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-27 23:27:44.830446 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-27 23:27:44.926844 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-27 23:27:45.030589 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-27 23:27:45.125948 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-27 23:27:45.226083 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-27 23:27:45.319167 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-27 23:27:45.421454 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-27 23:27:45.519168 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-27 23:27:45.615911 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-27 23:27:45.715121 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-27 23:27:45.820187 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-27 23:27:45.928964 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-27 23:27:46.034812 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-27 23:27:46.135228 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-27 23:27:46.236658 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-27 23:27:46.338142 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-27 23:27:46.442746 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-27 23:27:46.550967 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-27 23:27:46.819848 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-27 23:27:46.91166 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-27 23:27:47.010112 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-27 23:27:47.115465 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-27 23:27:47.220207 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-27 23:27:47.3215 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-27 23:27:47.416603 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-27 23:27:47.519935 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-27 23:27:47.622405 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-27 23:27:47.717662 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-27 23:27:47.820301 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-27 23:27:47.9117 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-27 23:27:48.003182 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-27 23:27:48.109876 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-27 23:27:48.205009 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-27 23:27:48.298551 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-27 23:27:48.401724 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-27 23:27:48.488685 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-27 23:27:48.579014 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-27 23:27:48.671035 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-27 23:27:48.7624 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-27 23:27:48.858516 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-27 23:27:48.966008 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-27 23:27:49.057709 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-27 23:27:49.163234 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-27 23:27:49.258557 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-27 23:27:49.360712 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-27 23:27:49.466244 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-27 23:27:49.56748 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-27 23:27:49.66991 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-27 23:27:49.775861 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-27 23:27:49.880938 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-27 23:27:49.975287 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-27 23:27:50.08483 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-27 23:27:50.177075 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-27 23:27:50.270143 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-27 23:27:50.360733 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-27 23:27:50.457188 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-27 23:27:50.548025 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-27 23:27:50.675861 INFO::Counting total values for each feature
2024-11-27 23:27:50.70379 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-11-27 23:27:50.793122 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-11-27 23:27:50.900605 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-11-27 23:27:51.002408 INFO::Writing residuals to file output/fits/residuals.rds
2024-11-27 23:27:51.039936 INFO::Writing fitted values to file output/fits/fitted.rds
2024-11-27 23:27:51.058727 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-11-27 23:27:51.063665 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-11-27 23:27:51.068934 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"
2024-11-27 23:27:51.080135 INFO::Writing function arguments to log file
2024-11-27 23:27:51.086693 INFO::Verifying options selected are valid
2024-11-27 23:27:51.087703 INFO::Determining format of input files
2024-11-27 23:27:51.088793 INFO::Input format is data samples as rows and metadata samples as rows
2024-11-27 23:27:51.093103 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-11-27 23:27:51.094117 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-11-27 23:27:51.095429 INFO::Filter data based on min abundance and min prevalence
2024-11-27 23:27:51.096212 INFO::Total samples in data: 1595
2024-11-27 23:27:51.097049 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-11-27 23:27:51.119628 INFO::Total filtered features: 0
2024-11-27 23:27:51.121029 INFO::Filtered feature names from abundance and prevalence filtering:
2024-11-27 23:27:51.126808 INFO::Total filtered features with variance filtering: 0
2024-11-27 23:27:51.127673 INFO::Filtered feature names from variance filtering:
2024-11-27 23:27:51.128432 INFO::Running selected normalization method: NONE
2024-11-27 23:27:51.129231 INFO::Bypass z-score application to metadata
2024-11-27 23:27:51.130051 INFO::Running selected transform method: AST
2024-11-27 23:27:51.141006 INFO::Running selected analysis method: LM
2024-11-27 23:27:51.142301 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-11-27 23:27:51.234742 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-11-27 23:27:51.332937 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-11-27 23:27:51.425934 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-11-27 23:27:51.517565 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-11-27 23:27:51.611379 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-11-27 23:27:51.699897 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-11-27 23:27:51.791914 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-11-27 23:27:51.88588 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-11-27 23:27:51.978326 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-11-27 23:27:52.079142 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-11-27 23:27:52.188987 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-11-27 23:27:52.283425 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-11-27 23:27:52.378452 WARNING::Fitting problem for feature 13 a warning was issued
2024-11-27 23:27:52.483485 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-11-27 23:27:52.579312 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-11-27 23:27:52.685015 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-11-27 23:27:52.77666 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-11-27 23:27:52.874244 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-11-27 23:27:52.975176 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-11-27 23:27:53.065594 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-11-27 23:27:53.15935 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-11-27 23:27:53.258669 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-11-27 23:27:53.347126 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-11-27 23:27:53.435446 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-11-27 23:27:53.537455 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-11-27 23:27:53.633182 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-11-27 23:27:53.743192 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-11-27 23:27:53.833847 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-11-27 23:27:53.918287 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-11-27 23:27:54.01053 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-11-27 23:27:54.100695 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-11-27 23:27:54.194622 INFO::Fitting model to feature number 32, Prevotella.copri
2024-11-27 23:27:54.295408 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-11-27 23:27:54.388956 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-11-27 23:27:54.483035 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-11-27 23:27:54.580756 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-11-27 23:27:54.673343 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-11-27 23:27:54.770868 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-11-27 23:27:54.857659 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-11-27 23:27:54.943095 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-11-27 23:27:55.036428 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-11-27 23:27:55.123485 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-11-27 23:27:55.221339 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-11-27 23:27:55.314142 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-11-27 23:27:55.407345 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-11-27 23:27:55.506303 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-11-27 23:27:55.600413 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-11-27 23:27:55.698123 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-11-27 23:27:55.792886 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-11-27 23:27:55.895515 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-11-27 23:27:55.982148 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-11-27 23:27:56.086179 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-11-27 23:27:56.174187 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-11-27 23:27:56.269428 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-11-27 23:27:56.362589 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-11-27 23:27:56.462971 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-11-27 23:27:56.558532 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-11-27 23:27:56.661453 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-11-27 23:27:56.763509 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-11-27 23:27:56.860532 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-11-27 23:27:56.959172 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-11-27 23:27:57.052447 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-11-27 23:27:57.158186 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-11-27 23:27:57.252044 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-11-27 23:27:57.359796 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-11-27 23:27:57.45376 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-11-27 23:27:57.553233 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-11-27 23:27:57.651831 WARNING::Fitting problem for feature 67 a warning was issued
2024-11-27 23:27:57.757503 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-11-27 23:27:57.854189 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-11-27 23:27:57.960792 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-11-27 23:27:58.061775 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-11-27 23:27:58.341145 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-11-27 23:27:58.377148 WARNING::Fitting problem for feature 72 a warning was issued
2024-11-27 23:27:58.477829 INFO::Fitting model to feature number 73, Dialister.invisus
2024-11-27 23:27:58.574987 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-11-27 23:27:58.675526 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-11-27 23:27:58.778457 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-11-27 23:27:58.879195 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-11-27 23:27:58.978527 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-11-27 23:27:59.081912 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-11-27 23:27:59.189812 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-11-27 23:27:59.285052 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-11-27 23:27:59.386942 INFO::Fitting model to feature number 82, Escherichia.coli
2024-11-27 23:27:59.487638 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-11-27 23:27:59.596696 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-11-27 23:27:59.695853 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-11-27 23:27:59.793621 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-11-27 23:27:59.897733 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-11-27 23:28:00.024281 INFO::Counting total values for each feature
2024-11-27 23:28:00.041153 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-11-27 23:28:00.136093 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-11-27 23:28:00.230225 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-11-27 23:28:00.34319 INFO::Writing residuals to file output2/fits/residuals.rds
2024-11-27 23:28:00.403607 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-11-27 23:28:00.458515 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-11-27 23:28:00.463736 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-11-27 23:28:00.46848 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 
 20.811   0.511  21.363

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin262.231 1.08563.577