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This page was generated on 2024-10-18 20:42 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1138/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.18.0  (landing page)
Lauren McIver
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on kjohnson1

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

raw results


Summary

Package: Maaslin2
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-10-18 02:19:39 -0400 (Fri, 18 Oct 2024)
EndedAt: 2024-10-18 02:22:41 -0400 (Fri, 18 Oct 2024)
EllapsedTime: 181.7 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 95.571  1.847  98.893
* 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-arm64/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 version 4.4.1 (2024-06-14) -- "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"
2024-10-18 02:21:55.106488 INFO::Writing function arguments to log file
2024-10-18 02:21:55.161908 INFO::Verifying options selected are valid
2024-10-18 02:21:55.210731 INFO::Determining format of input files
2024-10-18 02:21:55.212766 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-18 02:21:55.221831 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-18 02:21:55.223582 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-10-18 02:21:55.226273 INFO::Filter data based on min abundance and min prevalence
2024-10-18 02:21:55.227218 INFO::Total samples in data: 1595
2024-10-18 02:21:55.228077 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-18 02:21:55.2426 INFO::Total filtered features: 0
2024-10-18 02:21:55.24405 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-18 02:21:55.254394 INFO::Total filtered features with variance filtering: 0
2024-10-18 02:21:55.256031 INFO::Filtered feature names from variance filtering:
2024-10-18 02:21:55.256976 INFO::Running selected normalization method: TSS
2024-10-18 02:21:56.771181 INFO::Bypass z-score application to metadata
2024-10-18 02:21:56.772922 INFO::Running selected transform method: AST
2024-10-18 02:21:56.792853 INFO::Running selected analysis method: LM
2024-10-18 02:21:57.412419 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-18 02:21:57.875473 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-18 02:21:58.085723 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-18 02:21:58.264562 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-18 02:21:58.461958 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-18 02:21:58.642664 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-18 02:21:58.823568 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-18 02:21:59.008083 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-18 02:21:59.191374 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-18 02:21:59.389256 WARNING::Fitting problem for feature 9 a warning was issued
2024-10-18 02:21:59.578122 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-18 02:21:59.766356 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-18 02:21:59.94142 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-18 02:22:00.120676 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-18 02:22:00.295146 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-18 02:22:00.487518 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-18 02:22:00.673745 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-18 02:22:00.853276 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-18 02:22:01.037188 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-18 02:22:01.22555 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-18 02:22:01.389633 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-18 02:22:01.582261 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-18 02:22:01.77574 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-18 02:22:01.950297 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-18 02:22:02.134679 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-18 02:22:02.326808 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-18 02:22:02.512388 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-18 02:22:02.722359 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-18 02:22:02.89997 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-18 02:22:03.074729 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-18 02:22:03.267083 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-18 02:22:03.433408 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-18 02:22:03.622127 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-18 02:22:03.79756 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-18 02:22:03.996287 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-18 02:22:04.169868 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-18 02:22:04.358106 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-18 02:22:04.534236 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-18 02:22:04.722741 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-18 02:22:04.894101 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-18 02:22:05.075297 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-18 02:22:05.269042 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-18 02:22:05.441402 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-18 02:22:05.633387 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-18 02:22:05.813338 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-18 02:22:05.974823 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-18 02:22:06.17091 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-18 02:22:06.62726 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-18 02:22:06.800661 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-18 02:22:06.978689 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-18 02:22:07.161257 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-18 02:22:07.668704 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-18 02:22:07.845354 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-18 02:22:08.029195 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-18 02:22:08.225835 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-18 02:22:08.367853 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-18 02:22:08.47354 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-18 02:22:08.626183 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-18 02:22:08.695584 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-18 02:22:08.774621 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-18 02:22:08.927304 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-18 02:22:09.053254 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-18 02:22:09.195052 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-18 02:22:09.365022 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-18 02:22:09.538141 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-18 02:22:09.717968 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-18 02:22:09.930668 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-18 02:22:10.127257 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-18 02:22:10.291209 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-18 02:22:10.478526 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-18 02:22:10.658064 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-18 02:22:10.836766 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-18 02:22:11.025168 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-18 02:22:11.19828 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-18 02:22:11.379364 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-18 02:22:11.561028 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-18 02:22:11.739541 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-18 02:22:11.927492 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-18 02:22:12.100309 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-18 02:22:12.285515 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-18 02:22:12.474772 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-18 02:22:12.643106 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-18 02:22:12.839458 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-18 02:22:13.015524 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-18 02:22:13.185254 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-18 02:22:13.37346 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-18 02:22:13.540545 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-18 02:22:13.705967 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-18 02:22:13.939308 INFO::Counting total values for each feature
2024-10-18 02:22:13.979961 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-10-18 02:22:14.136681 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-10-18 02:22:14.31353 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-10-18 02:22:14.491501 INFO::Writing residuals to file output/fits/residuals.rds
2024-10-18 02:22:14.573411 INFO::Writing fitted values to file output/fits/fitted.rds
2024-10-18 02:22:14.618632 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-10-18 02:22:14.627978 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-10-18 02:22:14.636484 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"
2024-10-18 02:22:14.653836 INFO::Writing function arguments to log file
2024-10-18 02:22:14.660604 INFO::Verifying options selected are valid
2024-10-18 02:22:14.66167 INFO::Determining format of input files
2024-10-18 02:22:14.664123 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-18 02:22:14.671631 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-18 02:22:14.672971 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-10-18 02:22:14.67471 INFO::Filter data based on min abundance and min prevalence
2024-10-18 02:22:14.675615 INFO::Total samples in data: 1595
2024-10-18 02:22:14.67644 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-18 02:22:14.681501 INFO::Total filtered features: 0
2024-10-18 02:22:14.682662 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-18 02:22:14.707372 INFO::Total filtered features with variance filtering: 0
2024-10-18 02:22:14.709389 INFO::Filtered feature names from variance filtering:
2024-10-18 02:22:14.710734 INFO::Running selected normalization method: NONE
2024-10-18 02:22:14.711888 INFO::Bypass z-score application to metadata
2024-10-18 02:22:14.71271 INFO::Running selected transform method: AST
2024-10-18 02:22:14.730493 INFO::Running selected analysis method: LM
2024-10-18 02:22:14.732861 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-18 02:22:14.898939 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-18 02:22:15.076188 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-18 02:22:15.242628 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-18 02:22:15.422024 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-18 02:22:15.583783 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-18 02:22:15.755961 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-18 02:22:16.240964 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-18 02:22:16.409359 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-18 02:22:16.583716 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-18 02:22:16.766966 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-18 02:22:16.921557 WARNING::Fitting problem for feature 11 a warning was issued
2024-10-18 02:22:17.116284 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-18 02:22:17.277561 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-18 02:22:17.41477 WARNING::Fitting problem for feature 13 a warning was issued
2024-10-18 02:22:17.599606 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-18 02:22:17.766019 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-18 02:22:17.936336 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-18 02:22:18.100424 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-18 02:22:18.286841 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-18 02:22:18.457751 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-18 02:22:18.620759 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-18 02:22:19.112381 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-18 02:22:19.281502 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-18 02:22:19.452811 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-18 02:22:19.617909 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-18 02:22:19.805577 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-18 02:22:19.972952 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-18 02:22:20.164119 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-18 02:22:20.334049 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-18 02:22:20.513008 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-18 02:22:20.668169 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-18 02:22:20.835292 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-18 02:22:21.017536 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-18 02:22:21.196838 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-18 02:22:21.369867 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-18 02:22:21.545412 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-18 02:22:21.733264 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-18 02:22:21.909799 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-18 02:22:22.086164 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-18 02:22:22.257995 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-18 02:22:22.437402 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-18 02:22:22.604308 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-18 02:22:22.776374 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-18 02:22:22.959305 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-18 02:22:23.137118 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-18 02:22:23.311918 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-18 02:22:23.489113 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-18 02:22:23.69275 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-18 02:22:23.871245 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-18 02:22:24.044103 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-18 02:22:24.219153 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-18 02:22:24.374795 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-18 02:22:24.545505 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-18 02:22:24.700558 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-18 02:22:24.868288 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-18 02:22:25.036644 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-18 02:22:25.206925 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-18 02:22:25.3896 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-18 02:22:25.556376 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-18 02:22:25.726955 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-18 02:22:25.908289 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-18 02:22:26.071197 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-18 02:22:26.240858 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-18 02:22:26.414629 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-18 02:22:26.583541 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-18 02:22:26.747417 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-18 02:22:26.92215 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-18 02:22:27.086203 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-18 02:22:27.259682 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-18 02:22:27.430195 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-18 02:22:27.607462 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-18 02:22:27.796271 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-18 02:22:27.960621 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-18 02:22:28.020018 WARNING::Fitting problem for feature 72 a warning was issued
2024-10-18 02:22:28.223601 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-18 02:22:28.397205 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-18 02:22:28.567733 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-18 02:22:28.74196 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-18 02:22:28.926745 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-18 02:22:29.092801 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-18 02:22:29.275966 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-18 02:22:29.467023 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-18 02:22:29.631845 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-18 02:22:29.80959 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-18 02:22:29.976298 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-18 02:22:30.146855 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-18 02:22:30.311353 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-18 02:22:30.474487 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-18 02:22:30.661488 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-18 02:22:30.861883 INFO::Counting total values for each feature
2024-10-18 02:22:30.892983 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-10-18 02:22:31.045838 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-10-18 02:22:31.195946 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-10-18 02:22:31.381783 INFO::Writing residuals to file output2/fits/residuals.rds
2024-10-18 02:22:31.49366 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-10-18 02:22:31.598613 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-10-18 02:22:31.608164 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-10-18 02:22:31.615031 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 
 36.639   0.866  38.156

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin295.571 1.84798.893