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This page was generated on 2024-04-17 11:36:05 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1124/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.16.0  (landing page)
Lauren McIver
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_18
git_last_commit: 0ab531d
git_last_commit_date: 2023-10-24 11:15:22 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for Maaslin2 on nebbiolo2


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: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Maaslin2_1.16.0.tar.gz
StartedAt: 2024-04-16 00:23:08 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 00:28:44 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 336.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Maaslin2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.16.0’
* 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 loading without being on the library search path ... 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 83.564  1.268  84.773
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘maaslin2.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.10
Current TMB version is 1.9.11
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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"
2024-04-16 00:25:00.36842 INFO::Writing function arguments to log file
2024-04-16 00:25:00.405795 INFO::Verifying options selected are valid
2024-04-16 00:25:00.439929 INFO::Determining format of input files
2024-04-16 00:25:00.441322 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-16 00:25:00.445894 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-16 00:25:00.447164 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-04-16 00:25:00.449477 INFO::Filter data based on min abundance and min prevalence
2024-04-16 00:25:00.450365 INFO::Total samples in data: 1595
2024-04-16 00:25:00.451159 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-16 00:25:00.454773 INFO::Total filtered features: 0
2024-04-16 00:25:00.455728 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-16 00:25:00.462324 INFO::Total filtered features with variance filtering: 0
2024-04-16 00:25:00.463238 INFO::Filtered feature names from variance filtering:
2024-04-16 00:25:00.464016 INFO::Running selected normalization method: TSS
2024-04-16 00:25:01.582243 INFO::Bypass z-score application to metadata
2024-04-16 00:25:01.58348 INFO::Running selected transform method: AST
2024-04-16 00:25:01.598567 INFO::Running selected analysis method: LM
2024-04-16 00:25:02.139246 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-16 00:25:02.476588 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-16 00:25:02.642713 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-16 00:25:02.782509 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-16 00:25:02.924943 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-16 00:25:03.064336 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-16 00:25:03.210166 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-16 00:25:03.347958 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-16 00:25:03.461063 WARNING::Fitting problem for feature 8 a warning was issued
2024-04-16 00:25:03.62553 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-16 00:25:03.731906 WARNING::Fitting problem for feature 9 a warning was issued
2024-04-16 00:25:03.879021 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-16 00:25:04.013208 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-16 00:25:04.155011 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-16 00:25:04.285645 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-16 00:25:04.398185 WARNING::Fitting problem for feature 13 a warning was issued
2024-04-16 00:25:04.549502 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-16 00:25:04.687253 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-16 00:25:04.829391 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-16 00:25:04.964167 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-16 00:25:05.1095 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-16 00:25:05.249591 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-16 00:25:05.398573 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-16 00:25:05.572904 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-16 00:25:05.722834 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-16 00:25:05.865996 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-16 00:25:06.003994 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-16 00:25:06.141341 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-16 00:25:06.280864 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-16 00:25:06.421901 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-16 00:25:06.578232 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-16 00:25:06.730991 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-16 00:25:06.891069 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-16 00:25:07.036657 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-16 00:25:07.192867 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-16 00:25:07.354815 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-16 00:25:07.514027 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-16 00:25:07.651327 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-16 00:25:07.800091 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-16 00:25:07.939263 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-16 00:25:08.092313 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-16 00:25:08.237742 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-16 00:25:08.381327 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-16 00:25:08.537602 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-16 00:25:08.67479 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-16 00:25:08.827111 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-16 00:25:08.96484 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-16 00:25:09.10148 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-16 00:25:09.236525 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-16 00:25:09.381553 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-16 00:25:09.523254 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-16 00:25:09.69406 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-16 00:25:09.842521 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-16 00:25:09.985704 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-16 00:25:10.122619 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-16 00:25:10.267558 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-16 00:25:10.411644 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-16 00:25:10.554238 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-16 00:25:10.70344 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-16 00:25:10.84965 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-16 00:25:10.986171 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-16 00:25:11.164501 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-16 00:25:11.300682 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-16 00:25:11.437093 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-16 00:25:11.852754 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-16 00:25:11.993049 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-16 00:25:12.131348 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-16 00:25:12.2646 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-16 00:25:12.402248 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-16 00:25:12.535874 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-16 00:25:12.663517 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-16 00:25:12.815042 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-16 00:25:12.958708 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-16 00:25:13.098741 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-16 00:25:13.236059 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-16 00:25:13.371995 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-16 00:25:13.502774 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-16 00:25:13.643209 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-16 00:25:13.781458 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-16 00:25:13.917274 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-16 00:25:14.059105 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-16 00:25:14.222052 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-16 00:25:14.371797 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-16 00:25:14.523623 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-16 00:25:14.668209 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-16 00:25:14.805851 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-16 00:25:14.940422 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-16 00:25:15.073709 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-16 00:25:15.21156 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-16 00:25:15.345393 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-16 00:25:15.5292 INFO::Counting total values for each feature
2024-04-16 00:25:15.560957 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-04-16 00:25:15.706888 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-04-16 00:25:15.855559 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-04-16 00:25:16.006509 INFO::Writing residuals to file output/fits/residuals.rds
2024-04-16 00:25:16.062699 INFO::Writing fitted values to file output/fits/fitted.rds
2024-04-16 00:25:16.094155 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-04-16 00:25:16.099778 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-04-16 00:25:16.10637 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"
2024-04-16 00:25:16.120075 INFO::Writing function arguments to log file
2024-04-16 00:25:16.125752 INFO::Verifying options selected are valid
2024-04-16 00:25:16.126698 INFO::Determining format of input files
2024-04-16 00:25:16.12774 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-16 00:25:16.132718 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-16 00:25:16.133754 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-04-16 00:25:16.135398 INFO::Filter data based on min abundance and min prevalence
2024-04-16 00:25:16.136236 INFO::Total samples in data: 1595
2024-04-16 00:25:16.137037 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-16 00:25:16.141021 INFO::Total filtered features: 0
2024-04-16 00:25:16.141914 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-16 00:25:16.157482 INFO::Total filtered features with variance filtering: 0
2024-04-16 00:25:16.158568 INFO::Filtered feature names from variance filtering:
2024-04-16 00:25:16.159409 INFO::Running selected normalization method: NONE
2024-04-16 00:25:16.160218 INFO::Bypass z-score application to metadata
2024-04-16 00:25:16.161018 INFO::Running selected transform method: AST
2024-04-16 00:25:16.175169 INFO::Running selected analysis method: LM
2024-04-16 00:25:16.17673 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-16 00:25:16.308625 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-16 00:25:16.442735 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-16 00:25:16.567867 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-16 00:25:16.702554 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-16 00:25:16.827929 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-16 00:25:16.963959 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-16 00:25:17.092886 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-16 00:25:17.225678 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-16 00:25:17.36092 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-16 00:25:17.491426 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-16 00:25:17.626964 WARNING::Fitting problem for feature 11 a warning was issued
2024-04-16 00:25:17.772238 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-16 00:25:17.92138 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-16 00:25:18.058213 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-16 00:25:18.192841 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-16 00:25:18.334864 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-16 00:25:18.438572 WARNING::Fitting problem for feature 16 a warning was issued
2024-04-16 00:25:18.570822 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-16 00:25:18.715246 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-16 00:25:18.846649 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-16 00:25:18.972862 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-16 00:25:19.115103 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-16 00:25:19.249989 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-16 00:25:19.380868 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-16 00:25:19.523654 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-16 00:25:19.659121 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-16 00:25:19.794619 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-16 00:25:19.931933 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-16 00:25:20.064027 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-16 00:25:20.200942 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-16 00:25:20.324493 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-16 00:25:20.452688 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-16 00:25:20.588815 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-16 00:25:20.719019 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-16 00:25:20.845858 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-16 00:25:20.984199 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-16 00:25:21.110479 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-16 00:25:21.241945 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-16 00:25:21.37925 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-16 00:25:21.506344 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-16 00:25:21.628959 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-16 00:25:21.760156 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-16 00:25:21.902456 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-16 00:25:22.054521 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-16 00:25:22.190881 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-16 00:25:22.323153 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-16 00:25:22.458181 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-16 00:25:22.591847 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-16 00:25:22.72237 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-16 00:25:22.851379 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-16 00:25:22.984005 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-16 00:25:23.103078 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-16 00:25:23.463756 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-16 00:25:23.583795 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-16 00:25:23.704256 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-16 00:25:23.833911 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-16 00:25:23.970508 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-16 00:25:24.111548 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-16 00:25:24.239508 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-16 00:25:24.374368 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-16 00:25:24.512125 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-16 00:25:24.646582 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-16 00:25:24.789793 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-16 00:25:24.921807 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-16 00:25:25.055763 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-16 00:25:25.186956 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-16 00:25:25.318083 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-16 00:25:25.453853 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-16 00:25:25.563662 WARNING::Fitting problem for feature 67 a warning was issued
2024-04-16 00:25:25.703085 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-16 00:25:25.831372 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-16 00:25:25.969409 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-16 00:25:26.11526 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-16 00:25:26.247174 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-16 00:25:26.29273 WARNING::Fitting problem for feature 72 a warning was issued
2024-04-16 00:25:26.423329 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-16 00:25:26.554835 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-16 00:25:26.692477 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-16 00:25:26.820304 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-16 00:25:26.952603 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-16 00:25:27.082091 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-16 00:25:27.212435 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-16 00:25:27.352802 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-16 00:25:27.496546 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-16 00:25:27.642364 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-16 00:25:27.778378 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-16 00:25:27.920737 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-16 00:25:28.050538 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-16 00:25:28.179244 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-16 00:25:28.314878 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-16 00:25:28.492174 INFO::Counting total values for each feature
2024-04-16 00:25:28.514873 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-04-16 00:25:28.657502 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-04-16 00:25:28.799967 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-04-16 00:25:28.949133 INFO::Writing residuals to file output2/fits/residuals.rds
2024-04-16 00:25:29.023442 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-04-16 00:25:29.094788 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-04-16 00:25:29.100409 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-04-16 00:25:29.105627 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 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 29.188   0.677  29.857

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin283.564 1.26884.773