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This page was generated on 2025-04-02 19:30 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on palomino8

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: 1.20.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-04-01 03:00:02 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 03:03:31 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 208.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Maaslin2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.20.0'
* 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 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 113.54   7.04  120.97
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log'
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'Maaslin2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.16
Current TMB package version is 1.9.17
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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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"
2025-04-01 03:02:44.697541 INFO::Writing function arguments to log file
2025-04-01 03:02:44.748718 INFO::Verifying options selected are valid
2025-04-01 03:02:44.798209 INFO::Determining format of input files
2025-04-01 03:02:44.801712 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 03:02:44.81281 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 03:02:44.816278 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-04-01 03:02:44.821617 INFO::Filter data based on min abundance and min prevalence
2025-04-01 03:02:44.824433 INFO::Total samples in data: 1595
2025-04-01 03:02:44.83804 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 03:02:44.845284 INFO::Total filtered features: 0
2025-04-01 03:02:44.847286 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 03:02:44.856302 INFO::Total filtered features with variance filtering: 0
2025-04-01 03:02:44.858263 INFO::Filtered feature names from variance filtering:
2025-04-01 03:02:44.859949 INFO::Running selected normalization method: TSS
2025-04-01 03:02:46.259005 INFO::Bypass z-score application to metadata
2025-04-01 03:02:46.262132 INFO::Running selected transform method: AST
2025-04-01 03:02:46.289699 INFO::Running selected analysis method: LM
2025-04-01 03:02:46.713182 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 03:02:47.195326 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 03:02:47.405664 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 03:02:47.655532 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 03:02:47.889421 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 03:02:48.047996 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 03:02:48.213808 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 03:02:48.449786 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 03:02:48.622343 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 03:02:48.760382 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 03:02:48.942278 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 03:02:49.137701 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 03:02:49.322738 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 03:02:49.500301 WARNING::Fitting problem for feature 13 a warning was issued
2025-04-01 03:02:49.704919 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 03:02:49.843677 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 03:02:49.990069 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 03:02:50.168298 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 03:02:50.381059 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 03:02:50.614017 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 03:02:50.823434 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 03:02:51.079243 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 03:02:51.265841 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 03:02:51.469775 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 03:02:51.687711 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 03:02:51.916975 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 03:02:52.111462 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 03:02:52.256292 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 03:02:52.39428 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 03:02:52.585026 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 03:02:52.808978 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 03:02:53.027262 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 03:02:53.255281 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 03:02:53.47617 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 03:02:53.709467 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 03:02:54.161544 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 03:02:54.291305 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 03:02:54.422633 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 03:02:54.653484 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 03:02:54.804516 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 03:02:54.986457 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 03:02:55.180739 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 03:02:55.346903 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 03:02:55.509927 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 03:02:55.682497 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 03:02:55.901279 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 03:02:56.083409 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 03:02:56.262794 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 03:02:56.415017 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 03:02:56.615223 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 03:02:56.812347 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 03:02:57.030341 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 03:02:57.2391 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 03:02:57.451532 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 03:02:57.628686 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 03:02:57.798095 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 03:02:57.954604 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 03:02:58.173137 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 03:02:58.372439 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 03:02:58.613366 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 03:02:58.825972 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 03:02:59.038721 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 03:02:59.217175 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 03:02:59.458126 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 03:02:59.648152 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 03:02:59.807118 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 03:02:59.962842 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 03:03:00.155728 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 03:03:00.307346 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 03:03:00.47228 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 03:03:00.674947 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 03:03:00.844096 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 03:03:01.008833 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 03:03:01.203603 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 03:03:01.386388 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 03:03:01.543753 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 03:03:01.673968 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 03:03:01.84902 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 03:03:02.001574 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 03:03:02.136817 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 03:03:02.334335 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 03:03:02.558867 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 03:03:02.721485 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 03:03:02.865 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 03:03:02.993941 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 03:03:03.137562 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 03:03:03.285995 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 03:03:03.513534 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 03:03:03.819522 INFO::Counting total values for each feature
2025-04-01 03:03:03.876771 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-04-01 03:03:04.187934 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-04-01 03:03:04.547645 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-04-01 03:03:05.02536 INFO::Writing residuals to file output/fits/residuals.rds
2025-04-01 03:03:05.077542 INFO::Writing fitted values to file output/fits/fitted.rds
2025-04-01 03:03:05.115641 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-04-01 03:03:05.126752 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-04-01 03:03:05.151348 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"
2025-04-01 03:03:05.202299 INFO::Writing function arguments to log file
2025-04-01 03:03:05.217518 INFO::Verifying options selected are valid
2025-04-01 03:03:05.219554 INFO::Determining format of input files
2025-04-01 03:03:05.22172 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-01 03:03:05.232709 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-04-01 03:03:05.235682 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-04-01 03:03:05.239613 INFO::Filter data based on min abundance and min prevalence
2025-04-01 03:03:05.241294 INFO::Total samples in data: 1595
2025-04-01 03:03:05.242894 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-04-01 03:03:05.248784 INFO::Total filtered features: 0
2025-04-01 03:03:05.250576 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-01 03:03:05.268729 INFO::Total filtered features with variance filtering: 0
2025-04-01 03:03:05.271053 INFO::Filtered feature names from variance filtering:
2025-04-01 03:03:05.273049 INFO::Running selected normalization method: NONE
2025-04-01 03:03:05.274951 INFO::Bypass z-score application to metadata
2025-04-01 03:03:05.276857 INFO::Running selected transform method: AST
2025-04-01 03:03:05.292675 INFO::Running selected analysis method: LM
2025-04-01 03:03:05.295946 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-04-01 03:03:05.501056 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-04-01 03:03:05.693826 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-04-01 03:03:05.870357 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-04-01 03:03:06.076727 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-04-01 03:03:06.293932 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-04-01 03:03:06.499425 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-04-01 03:03:06.638599 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-04-01 03:03:06.769132 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-04-01 03:03:06.870399 WARNING::Fitting problem for feature 9 a warning was issued
2025-04-01 03:03:07.018328 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-04-01 03:03:07.202049 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-04-01 03:03:07.370744 WARNING::Fitting problem for feature 11 a warning was issued
2025-04-01 03:03:07.557063 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-04-01 03:03:07.685002 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-04-01 03:03:07.844654 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-04-01 03:03:08.029632 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-04-01 03:03:08.235548 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-04-01 03:03:08.380713 WARNING::Fitting problem for feature 16 a warning was issued
2025-04-01 03:03:08.57539 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-04-01 03:03:08.789266 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-04-01 03:03:08.971712 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-04-01 03:03:09.15447 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-04-01 03:03:09.657342 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-04-01 03:03:09.797833 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-04-01 03:03:09.968638 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-04-01 03:03:10.128187 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-04-01 03:03:10.276348 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-04-01 03:03:10.452597 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-04-01 03:03:10.657643 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-04-01 03:03:10.848609 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-04-01 03:03:11.005766 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-04-01 03:03:11.197964 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-04-01 03:03:11.402537 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-04-01 03:03:11.601724 INFO::Fitting model to feature number 32, Prevotella.copri
2025-04-01 03:03:11.769339 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-04-01 03:03:11.948664 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-04-01 03:03:12.109613 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-04-01 03:03:12.292327 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-04-01 03:03:12.445603 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-04-01 03:03:12.584281 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-04-01 03:03:12.758579 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-04-01 03:03:12.930448 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-04-01 03:03:13.051187 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-04-01 03:03:13.176123 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-04-01 03:03:13.30976 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-04-01 03:03:13.45685 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-04-01 03:03:13.637351 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-04-01 03:03:14.014695 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-04-01 03:03:14.151005 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-04-01 03:03:14.275455 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-04-01 03:03:14.404884 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-04-01 03:03:14.616483 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-04-01 03:03:14.782482 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-04-01 03:03:14.987259 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-04-01 03:03:15.114807 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-04-01 03:03:15.303187 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-04-01 03:03:15.503575 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-04-01 03:03:15.650726 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-04-01 03:03:15.826903 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-04-01 03:03:16.050829 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-04-01 03:03:16.209216 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-04-01 03:03:16.40497 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-04-01 03:03:16.55599 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-04-01 03:03:16.748806 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-04-01 03:03:16.922524 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-04-01 03:03:17.130231 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-04-01 03:03:17.30382 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-04-01 03:03:17.452335 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-04-01 03:03:17.599646 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-04-01 03:03:17.783957 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-04-01 03:03:17.973874 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-04-01 03:03:18.189488 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-04-01 03:03:18.391095 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-04-01 03:03:18.578678 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-04-01 03:03:18.623773 WARNING::Fitting problem for feature 72 a warning was issued
2025-04-01 03:03:18.760269 INFO::Fitting model to feature number 73, Dialister.invisus
2025-04-01 03:03:18.947773 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-04-01 03:03:19.069639 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-04-01 03:03:19.19706 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-04-01 03:03:19.362788 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-04-01 03:03:19.553517 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-04-01 03:03:19.69022 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-04-01 03:03:19.817015 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-04-01 03:03:19.958309 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-04-01 03:03:20.089675 INFO::Fitting model to feature number 82, Escherichia.coli
2025-04-01 03:03:20.20988 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-04-01 03:03:20.337585 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-04-01 03:03:20.485793 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-04-01 03:03:20.666694 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-04-01 03:03:20.866316 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-04-01 03:03:21.11125 INFO::Counting total values for each feature
2025-04-01 03:03:21.149345 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-04-01 03:03:21.500604 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-04-01 03:03:21.885131 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-04-01 03:03:22.287466 INFO::Writing residuals to file output2/fits/residuals.rds
2025-04-01 03:03:22.35984 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-04-01 03:03:22.416471 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-04-01 03:03:22.423197 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-04-01 03:03:22.435091 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 
  38.04    1.26   39.31

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2113.54 7.04120.97