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This page was generated on 2024-04-17 11:36:56 -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 palomino4


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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Maaslin2_1.16.0.tar.gz
StartedAt: 2024-04-16 02:11:53 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 02:15:02 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 188.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Maaslin2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/Maaslin2.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 100.5   6.66  108.12
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 02:14:19.256036 INFO::Writing function arguments to log file
2024-04-16 02:14:19.291564 INFO::Verifying options selected are valid
2024-04-16 02:14:19.325316 INFO::Determining format of input files
2024-04-16 02:14:19.327748 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-16 02:14:19.334729 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-16 02:14:19.336877 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-04-16 02:14:19.340163 INFO::Filter data based on min abundance and min prevalence
2024-04-16 02:14:19.341895 INFO::Total samples in data: 1595
2024-04-16 02:14:19.34358 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-16 02:14:19.349138 INFO::Total filtered features: 0
2024-04-16 02:14:19.351088 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-16 02:14:19.359781 INFO::Total filtered features with variance filtering: 0
2024-04-16 02:14:19.36188 INFO::Filtered feature names from variance filtering:
2024-04-16 02:14:19.3637 INFO::Running selected normalization method: TSS
2024-04-16 02:14:20.44895 INFO::Bypass z-score application to metadata
2024-04-16 02:14:20.451111 INFO::Running selected transform method: AST
2024-04-16 02:14:20.477005 INFO::Running selected analysis method: LM
2024-04-16 02:14:21.019364 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-16 02:14:21.394055 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-16 02:14:21.570048 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-16 02:14:21.705064 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-16 02:14:21.858237 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-16 02:14:22.03883 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-16 02:14:22.188063 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-16 02:14:22.32174 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-16 02:14:22.461775 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-16 02:14:22.595423 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-16 02:14:22.735967 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-16 02:14:22.867895 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-16 02:14:23.003187 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-16 02:14:23.158607 WARNING::Fitting problem for feature 13 a warning was issued
2024-04-16 02:14:23.305145 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-16 02:14:23.455449 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-16 02:14:23.645787 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-16 02:14:23.800948 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-16 02:14:23.944745 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-16 02:14:24.080348 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-16 02:14:24.232675 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-16 02:14:24.368204 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-16 02:14:24.504252 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-16 02:14:24.64948 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-16 02:14:24.780105 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-16 02:14:24.915154 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-16 02:14:25.062413 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-16 02:14:25.206846 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-16 02:14:25.374547 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-16 02:14:25.519304 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-16 02:14:25.662743 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-16 02:14:25.797006 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-16 02:14:25.940725 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-16 02:14:26.080527 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-16 02:14:26.254167 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-16 02:14:26.407037 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-16 02:14:26.540614 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-16 02:14:26.674237 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-16 02:14:26.851262 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-16 02:14:27.02123 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-16 02:14:27.157761 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-16 02:14:27.300328 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-16 02:14:27.434118 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-16 02:14:27.578277 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-16 02:14:27.709754 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-16 02:14:27.903256 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-16 02:14:28.099078 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-16 02:14:28.268962 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-16 02:14:28.496514 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-16 02:14:28.651485 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-16 02:14:28.792724 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-16 02:14:28.930871 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-16 02:14:29.09088 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-16 02:14:29.254492 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-16 02:14:29.491852 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-16 02:14:29.65612 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-16 02:14:29.843592 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-16 02:14:30.06062 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-16 02:14:30.254637 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-16 02:14:30.494847 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-16 02:14:30.700662 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-16 02:14:30.839445 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-16 02:14:30.997171 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-16 02:14:31.156389 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-16 02:14:31.603748 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-16 02:14:31.743274 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-16 02:14:31.907035 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-16 02:14:32.12839 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-16 02:14:32.283152 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-16 02:14:32.469949 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-16 02:14:32.903183 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-16 02:14:33.073992 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-16 02:14:33.23943 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-16 02:14:33.443212 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-16 02:14:33.616288 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-16 02:14:33.764873 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-16 02:14:33.911301 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-16 02:14:34.051754 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-16 02:14:34.192666 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-16 02:14:34.335508 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-16 02:14:34.534312 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-16 02:14:34.718177 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-16 02:14:34.86861 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-16 02:14:35.043037 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-16 02:14:35.256621 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-16 02:14:35.468844 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-16 02:14:35.690188 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-16 02:14:35.900906 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-16 02:14:36.187615 INFO::Counting total values for each feature
2024-04-16 02:14:36.242727 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-04-16 02:14:36.649036 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-04-16 02:14:37.029064 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-04-16 02:14:37.457731 INFO::Writing residuals to file output/fits/residuals.rds
2024-04-16 02:14:37.510286 INFO::Writing fitted values to file output/fits/fitted.rds
2024-04-16 02:14:37.539685 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-04-16 02:14:37.548855 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-04-16 02:14:37.569235 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 02:14:37.608494 INFO::Writing function arguments to log file
2024-04-16 02:14:37.630003 INFO::Verifying options selected are valid
2024-04-16 02:14:37.632892 INFO::Determining format of input files
2024-04-16 02:14:37.635955 INFO::Input format is data samples as rows and metadata samples as rows
2024-04-16 02:14:37.6458 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-04-16 02:14:37.649028 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-04-16 02:14:37.652924 INFO::Filter data based on min abundance and min prevalence
2024-04-16 02:14:37.655593 INFO::Total samples in data: 1595
2024-04-16 02:14:37.657744 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-04-16 02:14:37.663935 INFO::Total filtered features: 0
2024-04-16 02:14:37.666528 INFO::Filtered feature names from abundance and prevalence filtering:
2024-04-16 02:14:37.67507 INFO::Total filtered features with variance filtering: 0
2024-04-16 02:14:37.677149 INFO::Filtered feature names from variance filtering:
2024-04-16 02:14:37.67884 INFO::Running selected normalization method: NONE
2024-04-16 02:14:37.6808 INFO::Bypass z-score application to metadata
2024-04-16 02:14:37.683462 INFO::Running selected transform method: AST
2024-04-16 02:14:37.706319 INFO::Running selected analysis method: LM
2024-04-16 02:14:37.708857 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-04-16 02:14:37.85733 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-04-16 02:14:38.023809 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-04-16 02:14:38.164131 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-04-16 02:14:38.307845 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-04-16 02:14:38.427072 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-04-16 02:14:38.576093 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-04-16 02:14:38.752247 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-04-16 02:14:38.912318 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-04-16 02:14:39.02145 WARNING::Fitting problem for feature 9 a warning was issued
2024-04-16 02:14:39.24838 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-04-16 02:14:39.462633 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-04-16 02:14:39.60813 WARNING::Fitting problem for feature 11 a warning was issued
2024-04-16 02:14:39.767254 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-04-16 02:14:39.974747 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-04-16 02:14:40.190376 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-04-16 02:14:40.326452 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-04-16 02:14:40.501294 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-04-16 02:14:40.654843 WARNING::Fitting problem for feature 16 a warning was issued
2024-04-16 02:14:40.808571 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-04-16 02:14:40.942447 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-04-16 02:14:41.072257 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-04-16 02:14:41.214296 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-04-16 02:14:41.33445 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-04-16 02:14:41.476963 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-04-16 02:14:41.648449 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-04-16 02:14:41.764878 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-04-16 02:14:41.922504 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-04-16 02:14:42.123216 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-04-16 02:14:42.312398 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-04-16 02:14:42.537324 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-04-16 02:14:42.728898 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-04-16 02:14:42.927649 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-04-16 02:14:43.117597 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-04-16 02:14:43.305212 INFO::Fitting model to feature number 32, Prevotella.copri
2024-04-16 02:14:43.689251 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-04-16 02:14:43.809874 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-04-16 02:14:43.93528 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-04-16 02:14:44.076153 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-04-16 02:14:44.20669 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-04-16 02:14:44.354851 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-04-16 02:14:44.480188 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-04-16 02:14:44.611861 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-04-16 02:14:44.73213 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-04-16 02:14:44.854849 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-04-16 02:14:45.015823 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-04-16 02:14:45.188436 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-04-16 02:14:45.392472 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-04-16 02:14:45.527671 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-04-16 02:14:45.731718 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-04-16 02:14:45.915787 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-04-16 02:14:46.110822 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-04-16 02:14:46.298197 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-04-16 02:14:46.7222 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-04-16 02:14:46.887562 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-04-16 02:14:47.005407 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-04-16 02:14:47.134858 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-04-16 02:14:47.295575 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-04-16 02:14:47.486494 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-04-16 02:14:47.6814 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-04-16 02:14:47.869255 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-04-16 02:14:47.990529 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-04-16 02:14:48.113658 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-04-16 02:14:48.251135 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-04-16 02:14:48.435876 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-04-16 02:14:48.618118 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-04-16 02:14:48.800865 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-04-16 02:14:48.98338 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-04-16 02:14:49.10577 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-04-16 02:14:49.231331 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-04-16 02:14:49.40488 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-04-16 02:14:49.550946 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-04-16 02:14:49.772204 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-04-16 02:14:49.913202 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-04-16 02:14:50.061588 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-04-16 02:14:50.11042 WARNING::Fitting problem for feature 72 a warning was issued
2024-04-16 02:14:50.278062 INFO::Fitting model to feature number 73, Dialister.invisus
2024-04-16 02:14:50.421041 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-04-16 02:14:50.542506 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-04-16 02:14:50.687066 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-04-16 02:14:50.858155 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-04-16 02:14:50.978492 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-04-16 02:14:51.130032 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-04-16 02:14:51.336749 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-04-16 02:14:51.483794 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-04-16 02:14:51.665703 INFO::Fitting model to feature number 82, Escherichia.coli
2024-04-16 02:14:51.785339 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-04-16 02:14:51.916208 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-04-16 02:14:52.094442 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-04-16 02:14:52.254148 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-04-16 02:14:52.410923 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-04-16 02:14:52.559652 INFO::Counting total values for each feature
2024-04-16 02:14:52.585279 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-04-16 02:14:52.843291 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-04-16 02:14:53.110377 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-04-16 02:14:53.635709 INFO::Writing residuals to file output2/fits/residuals.rds
2024-04-16 02:14:53.715963 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-04-16 02:14:53.792133 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-04-16 02:14:53.801548 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-04-16 02:14:53.822007 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 5 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
  35.20    0.65   35.89

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2100.50 6.66108.12