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This page was generated on 2024-10-18 11:44 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4474
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4733
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4479
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4509
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4457
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 1125/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.19.0  (landing page)
Lauren McIver
Snapshot Date: 2024-10-17 13:40 -0400 (Thu, 17 Oct 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 2f9ea7a
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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 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: 1.19.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.19.0.tar.gz
StartedAt: 2024-10-18 02:57:53 -0400 (Fri, 18 Oct 2024)
EndedAt: 2024-10-18 03:05:18 -0400 (Fri, 18 Oct 2024)
EllapsedTime: 444.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Maaslin2_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.19.0’
* 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'
 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 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 76.839  0.648  77.477
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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: x86_64-pc-linux-gnu

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 03:03:19.222943 INFO::Writing function arguments to log file
2024-10-18 03:03:19.25773 INFO::Verifying options selected are valid
2024-10-18 03:03:19.28753 INFO::Determining format of input files
2024-10-18 03:03:19.288788 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-18 03:03:19.293058 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-18 03:03:19.294167 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-10-18 03:03:19.296329 INFO::Filter data based on min abundance and min prevalence
2024-10-18 03:03:19.297134 INFO::Total samples in data: 1595
2024-10-18 03:03:19.297915 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-18 03:03:19.301311 INFO::Total filtered features: 0
2024-10-18 03:03:19.302228 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-18 03:03:19.313944 INFO::Total filtered features with variance filtering: 0
2024-10-18 03:03:19.314845 INFO::Filtered feature names from variance filtering:
2024-10-18 03:03:19.315639 INFO::Running selected normalization method: TSS
2024-10-18 03:03:20.29757 INFO::Bypass z-score application to metadata
2024-10-18 03:03:20.299075 INFO::Running selected transform method: AST
2024-10-18 03:03:20.31577 INFO::Running selected analysis method: LM
2024-10-18 03:03:20.779338 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-18 03:03:21.095356 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-18 03:03:21.234885 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-18 03:03:21.37331 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-18 03:03:21.518159 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-18 03:03:21.653251 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-18 03:03:21.78957 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-18 03:03:21.927955 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-18 03:03:22.032593 WARNING::Fitting problem for feature 8 a warning was issued
2024-10-18 03:03:22.170708 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-18 03:03:22.274107 WARNING::Fitting problem for feature 9 a warning was issued
2024-10-18 03:03:22.421152 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-18 03:03:22.552071 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-18 03:03:22.685095 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-18 03:03:22.840069 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-18 03:03:22.951241 WARNING::Fitting problem for feature 13 a warning was issued
2024-10-18 03:03:23.091152 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-18 03:03:23.22288 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-18 03:03:23.362604 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-18 03:03:23.493522 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-18 03:03:23.62777 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-18 03:03:23.76802 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-18 03:03:23.892419 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-18 03:03:24.01893 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-18 03:03:24.189184 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-18 03:03:24.328769 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-18 03:03:24.463539 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-18 03:03:24.599267 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-18 03:03:24.735986 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-18 03:03:24.863005 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-18 03:03:25.003344 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-18 03:03:25.147669 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-18 03:03:25.285556 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-18 03:03:25.415355 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-18 03:03:25.558679 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-18 03:03:25.692263 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-18 03:03:25.840157 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-18 03:03:26.211031 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-18 03:03:26.343035 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-18 03:03:26.479721 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-18 03:03:26.618747 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-18 03:03:26.743391 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-18 03:03:26.878148 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-18 03:03:27.026875 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-18 03:03:27.159014 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-18 03:03:27.293604 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-18 03:03:27.420264 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-18 03:03:27.548301 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-18 03:03:27.678555 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-18 03:03:27.811945 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-18 03:03:27.952432 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-18 03:03:28.079749 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-18 03:03:28.210469 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-18 03:03:28.34321 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-18 03:03:28.468745 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-18 03:03:28.617203 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-18 03:03:28.777982 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-18 03:03:28.91207 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-18 03:03:29.053556 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-18 03:03:29.200442 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-18 03:03:29.326847 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-18 03:03:29.467593 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-18 03:03:29.595104 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-18 03:03:29.72169 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-18 03:03:29.856582 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-18 03:03:29.995678 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-18 03:03:30.131523 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-18 03:03:30.266903 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-18 03:03:30.391138 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-18 03:03:30.52446 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-18 03:03:30.64398 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-18 03:03:30.777844 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-18 03:03:30.914241 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-18 03:03:31.049618 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-18 03:03:31.178969 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-18 03:03:31.306523 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-18 03:03:31.436978 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-18 03:03:31.56462 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-18 03:03:31.706887 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-18 03:03:31.837997 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-18 03:03:31.970784 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-18 03:03:32.374426 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-18 03:03:32.509941 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-18 03:03:32.644068 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-18 03:03:32.784105 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-18 03:03:32.933884 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-18 03:03:33.058716 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-18 03:03:33.18572 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-18 03:03:33.31287 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-18 03:03:33.440799 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-18 03:03:33.611995 INFO::Counting total values for each feature
2024-10-18 03:03:33.641082 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-10-18 03:03:33.737431 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-10-18 03:03:33.833549 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-10-18 03:03:33.931939 INFO::Writing residuals to file output/fits/residuals.rds
2024-10-18 03:03:33.980099 INFO::Writing fitted values to file output/fits/fitted.rds
2024-10-18 03:03:34.006872 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-10-18 03:03:34.012047 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-10-18 03:03:34.016896 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 03:03:34.029039 INFO::Writing function arguments to log file
2024-10-18 03:03:34.034581 INFO::Verifying options selected are valid
2024-10-18 03:03:34.035451 INFO::Determining format of input files
2024-10-18 03:03:34.036476 INFO::Input format is data samples as rows and metadata samples as rows
2024-10-18 03:03:34.041022 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-10-18 03:03:34.041992 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-10-18 03:03:34.043519 INFO::Filter data based on min abundance and min prevalence
2024-10-18 03:03:34.044326 INFO::Total samples in data: 1595
2024-10-18 03:03:34.045121 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-10-18 03:03:34.049345 INFO::Total filtered features: 0
2024-10-18 03:03:34.050234 INFO::Filtered feature names from abundance and prevalence filtering:
2024-10-18 03:03:34.057228 INFO::Total filtered features with variance filtering: 0
2024-10-18 03:03:34.058088 INFO::Filtered feature names from variance filtering:
2024-10-18 03:03:34.058874 INFO::Running selected normalization method: NONE
2024-10-18 03:03:34.059637 INFO::Bypass z-score application to metadata
2024-10-18 03:03:34.060432 INFO::Running selected transform method: AST
2024-10-18 03:03:34.084347 INFO::Running selected analysis method: LM
2024-10-18 03:03:34.085716 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-10-18 03:03:34.214198 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-10-18 03:03:34.339311 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-10-18 03:03:34.461362 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-10-18 03:03:34.596471 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-10-18 03:03:34.718523 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-10-18 03:03:34.847935 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-10-18 03:03:34.973491 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-10-18 03:03:35.104114 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-10-18 03:03:35.227745 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-10-18 03:03:35.355412 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-10-18 03:03:35.462475 WARNING::Fitting problem for feature 11 a warning was issued
2024-10-18 03:03:35.601579 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-10-18 03:03:35.721959 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-10-18 03:03:35.847282 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-10-18 03:03:35.977889 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-10-18 03:03:36.104535 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-10-18 03:03:36.205405 WARNING::Fitting problem for feature 16 a warning was issued
2024-10-18 03:03:36.334273 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-10-18 03:03:36.468656 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-10-18 03:03:36.594705 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-10-18 03:03:36.732986 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-10-18 03:03:36.883205 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-10-18 03:03:37.015789 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-10-18 03:03:37.147156 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-10-18 03:03:37.272497 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-10-18 03:03:37.398472 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-10-18 03:03:37.523557 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-10-18 03:03:37.652549 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-10-18 03:03:37.778039 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-10-18 03:03:37.897304 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-10-18 03:03:38.021833 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-10-18 03:03:38.141113 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-10-18 03:03:38.262636 INFO::Fitting model to feature number 32, Prevotella.copri
2024-10-18 03:03:38.392741 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-10-18 03:03:38.513282 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-10-18 03:03:38.642965 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-10-18 03:03:38.770758 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-10-18 03:03:38.900929 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-10-18 03:03:39.04144 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-10-18 03:03:39.168202 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-10-18 03:03:39.290191 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-10-18 03:03:39.414855 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-10-18 03:03:39.537138 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-10-18 03:03:39.664732 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-10-18 03:03:39.790088 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-10-18 03:03:39.921379 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-10-18 03:03:40.044648 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-10-18 03:03:40.18009 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-10-18 03:03:40.300669 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-10-18 03:03:40.658709 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-10-18 03:03:40.783594 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-10-18 03:03:40.900011 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-10-18 03:03:41.02834 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-10-18 03:03:41.147117 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-10-18 03:03:41.271162 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-10-18 03:03:41.391326 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-10-18 03:03:41.511072 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-10-18 03:03:41.633927 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-10-18 03:03:41.771789 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-10-18 03:03:41.894927 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-10-18 03:03:42.022073 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-10-18 03:03:42.147501 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-10-18 03:03:42.274063 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-10-18 03:03:42.404301 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-10-18 03:03:42.529836 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-10-18 03:03:42.654276 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-10-18 03:03:42.780059 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-10-18 03:03:42.910454 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-10-18 03:03:43.014981 WARNING::Fitting problem for feature 67 a warning was issued
2024-10-18 03:03:43.147554 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-10-18 03:03:43.269994 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-10-18 03:03:43.402175 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-10-18 03:03:43.542077 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-10-18 03:03:43.667053 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-10-18 03:03:43.71043 WARNING::Fitting problem for feature 72 a warning was issued
2024-10-18 03:03:43.836532 INFO::Fitting model to feature number 73, Dialister.invisus
2024-10-18 03:03:43.965005 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-10-18 03:03:44.098432 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-10-18 03:03:44.223642 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-10-18 03:03:44.351737 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-10-18 03:03:44.477292 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-10-18 03:03:44.6096 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-10-18 03:03:44.740376 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-10-18 03:03:44.864114 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-10-18 03:03:44.995621 INFO::Fitting model to feature number 82, Escherichia.coli
2024-10-18 03:03:45.119554 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-10-18 03:03:45.247116 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-10-18 03:03:45.368576 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-10-18 03:03:45.491464 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-10-18 03:03:45.621455 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-10-18 03:03:45.779786 INFO::Counting total values for each feature
2024-10-18 03:03:45.800874 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-10-18 03:03:45.894187 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-10-18 03:03:45.987655 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-10-18 03:03:46.085625 INFO::Writing residuals to file output2/fits/residuals.rds
2024-10-18 03:03:46.148892 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-10-18 03:03:46.210181 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-10-18 03:03:46.21531 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-10-18 03:03:46.219339 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 
 27.381   0.599  27.971

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin276.839 0.64877.477