Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-03-19 11:44 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1141/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.21.0  (landing page)
Lauren McIver
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: devel
git_last_commit: 3dacd30
git_last_commit_date: 2024-10-29 10:38:48 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on lconway

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: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
StartedAt: 2025-03-18 21:48:02 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 21:51:01 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 179.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.21.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 95.886  1.859  98.564
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** this is package ‘Maaslin2’ version ‘1.21.0’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-03-18 21:50:19.827634 INFO::Writing function arguments to log file
2025-03-18 21:50:19.883155 INFO::Verifying options selected are valid
2025-03-18 21:50:19.921524 INFO::Determining format of input files
2025-03-18 21:50:19.923996 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 21:50:19.933403 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 21:50:19.935888 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-03-18 21:50:19.94007 INFO::Filter data based on min abundance and min prevalence
2025-03-18 21:50:19.941835 INFO::Total samples in data: 1595
2025-03-18 21:50:19.943522 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 21:50:19.958147 INFO::Total filtered features: 0
2025-03-18 21:50:19.960371 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 21:50:19.971085 INFO::Total filtered features with variance filtering: 0
2025-03-18 21:50:19.972968 INFO::Filtered feature names from variance filtering:
2025-03-18 21:50:19.974451 INFO::Running selected normalization method: TSS
2025-03-18 21:50:21.276818 INFO::Bypass z-score application to metadata
2025-03-18 21:50:21.278521 INFO::Running selected transform method: AST
2025-03-18 21:50:21.299375 INFO::Running selected analysis method: LM
2025-03-18 21:50:21.929687 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 21:50:22.377502 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 21:50:22.562997 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 21:50:22.779887 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 21:50:22.943075 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 21:50:23.109882 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 21:50:23.283973 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 21:50:23.465017 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 21:50:23.63341 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 21:50:23.804266 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 21:50:23.984744 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 21:50:24.145598 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 21:50:24.305486 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 21:50:24.448841 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 21:50:24.625784 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 21:50:24.785684 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 21:50:25.000484 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 21:50:25.145255 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 21:50:25.317535 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 21:50:25.488405 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 21:50:25.660806 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 21:50:25.82925 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 21:50:25.99635 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 21:50:26.160665 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 21:50:26.311175 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 21:50:26.48397 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 21:50:26.673775 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 21:50:26.837536 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 21:50:27.012208 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 21:50:27.188595 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 21:50:27.353255 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 21:50:27.518851 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 21:50:27.695441 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 21:50:27.86557 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 21:50:28.015161 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 21:50:28.168394 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 21:50:28.337927 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 21:50:28.506466 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 21:50:28.682286 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 21:50:28.866048 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 21:50:29.052854 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 21:50:29.231984 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 21:50:29.396504 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 21:50:29.565668 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 21:50:29.746652 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 21:50:29.912093 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 21:50:30.072028 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 21:50:30.237079 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 21:50:30.426764 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 21:50:30.580159 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 21:50:30.751295 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 21:50:30.905296 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 21:50:31.070084 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 21:50:31.229451 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 21:50:31.409731 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 21:50:31.571489 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 21:50:31.739647 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 21:50:31.891642 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 21:50:32.048428 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 21:50:32.199304 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 21:50:32.386084 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 21:50:32.544641 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 21:50:32.694724 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 21:50:32.868929 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 21:50:33.034223 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 21:50:33.18599 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 21:50:33.35983 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 21:50:33.531848 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 21:50:33.697321 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 21:50:34.093444 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 21:50:34.256231 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 21:50:34.413471 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 21:50:34.570596 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 21:50:34.740861 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 21:50:34.900063 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 21:50:35.061275 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 21:50:35.242192 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 21:50:35.385476 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 21:50:35.544875 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 21:50:35.723163 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 21:50:36.145374 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 21:50:36.299722 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 21:50:36.466022 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 21:50:36.629371 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 21:50:36.812677 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 21:50:36.965194 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 21:50:37.105255 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 21:50:37.26673 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 21:50:37.469159 INFO::Counting total values for each feature
2025-03-18 21:50:37.502574 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-03-18 21:50:37.627001 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-03-18 21:50:37.77141 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-03-18 21:50:37.911014 INFO::Writing residuals to file output/fits/residuals.rds
2025-03-18 21:50:37.971556 INFO::Writing fitted values to file output/fits/fitted.rds
2025-03-18 21:50:37.997821 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-03-18 21:50:38.005802 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-03-18 21:50:38.015301 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"
2025-03-18 21:50:38.034186 INFO::Writing function arguments to log file
2025-03-18 21:50:38.04498 INFO::Verifying options selected are valid
2025-03-18 21:50:38.046115 INFO::Determining format of input files
2025-03-18 21:50:38.047414 INFO::Input format is data samples as rows and metadata samples as rows
2025-03-18 21:50:38.053725 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-03-18 21:50:38.055584 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-03-18 21:50:38.058229 INFO::Filter data based on min abundance and min prevalence
2025-03-18 21:50:38.059504 INFO::Total samples in data: 1595
2025-03-18 21:50:38.060622 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-03-18 21:50:38.066187 INFO::Total filtered features: 0
2025-03-18 21:50:38.068414 INFO::Filtered feature names from abundance and prevalence filtering:
2025-03-18 21:50:38.077865 INFO::Total filtered features with variance filtering: 0
2025-03-18 21:50:38.079322 INFO::Filtered feature names from variance filtering:
2025-03-18 21:50:38.080455 INFO::Running selected normalization method: NONE
2025-03-18 21:50:38.081588 INFO::Bypass z-score application to metadata
2025-03-18 21:50:38.083151 INFO::Running selected transform method: AST
2025-03-18 21:50:38.114525 INFO::Running selected analysis method: LM
2025-03-18 21:50:38.117467 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-03-18 21:50:38.272634 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-03-18 21:50:38.421043 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-03-18 21:50:38.553723 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-03-18 21:50:38.721865 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-03-18 21:50:38.879071 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-03-18 21:50:39.030059 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-03-18 21:50:39.170646 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-03-18 21:50:39.339102 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-03-18 21:50:39.470267 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-03-18 21:50:39.620986 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-03-18 21:50:39.77336 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-03-18 21:50:39.921471 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-03-18 21:50:40.048854 WARNING::Fitting problem for feature 13 a warning was issued
2025-03-18 21:50:40.19968 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-03-18 21:50:40.354623 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-03-18 21:50:40.498499 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-03-18 21:50:40.644864 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-03-18 21:50:40.802669 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-03-18 21:50:40.976576 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-03-18 21:50:41.114259 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-03-18 21:50:41.265662 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-03-18 21:50:41.413327 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-03-18 21:50:41.575047 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-03-18 21:50:41.712974 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-03-18 21:50:41.870357 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-03-18 21:50:42.028969 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-03-18 21:50:42.158809 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-03-18 21:50:42.318373 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-03-18 21:50:42.455753 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-03-18 21:50:42.595439 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-03-18 21:50:42.737697 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-03-18 21:50:42.902353 INFO::Fitting model to feature number 32, Prevotella.copri
2025-03-18 21:50:43.063392 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-03-18 21:50:43.204309 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-03-18 21:50:43.378456 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-03-18 21:50:43.524134 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-03-18 21:50:43.68569 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-03-18 21:50:43.854946 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-03-18 21:50:44.016606 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-03-18 21:50:44.17075 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-03-18 21:50:44.323408 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-03-18 21:50:44.483176 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-03-18 21:50:44.644329 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-03-18 21:50:44.805217 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-03-18 21:50:44.97392 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-03-18 21:50:45.132232 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-03-18 21:50:45.270393 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-03-18 21:50:45.427619 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-03-18 21:50:45.588258 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-03-18 21:50:45.751737 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-03-18 21:50:45.895788 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-03-18 21:50:46.079314 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-03-18 21:50:46.22534 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-03-18 21:50:46.381952 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-03-18 21:50:46.517355 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-03-18 21:50:46.65185 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-03-18 21:50:46.795643 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-03-18 21:50:46.969571 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-03-18 21:50:47.116672 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-03-18 21:50:47.254673 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-03-18 21:50:47.39706 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-03-18 21:50:47.558658 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-03-18 21:50:47.693727 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-03-18 21:50:47.852842 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-03-18 21:50:48.002272 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-03-18 21:50:48.166627 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-03-18 21:50:48.305198 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-03-18 21:50:48.421752 WARNING::Fitting problem for feature 67 a warning was issued
2025-03-18 21:50:48.574821 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-03-18 21:50:48.724336 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-03-18 21:50:48.875884 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-03-18 21:50:49.018023 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-03-18 21:50:49.163803 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-03-18 21:50:49.221877 WARNING::Fitting problem for feature 72 a warning was issued
2025-03-18 21:50:49.374499 INFO::Fitting model to feature number 73, Dialister.invisus
2025-03-18 21:50:49.531287 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-03-18 21:50:49.680082 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-03-18 21:50:49.840083 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-03-18 21:50:50.021109 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-03-18 21:50:50.170826 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-03-18 21:50:50.311801 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-03-18 21:50:50.464609 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-03-18 21:50:50.619914 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-03-18 21:50:50.773564 INFO::Fitting model to feature number 82, Escherichia.coli
2025-03-18 21:50:50.934885 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-03-18 21:50:51.100018 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-03-18 21:50:51.254449 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-03-18 21:50:51.401743 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-03-18 21:50:51.5699 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-03-18 21:50:51.773011 INFO::Counting total values for each feature
2025-03-18 21:50:51.799362 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-03-18 21:50:51.927843 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-03-18 21:50:52.069551 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-03-18 21:50:52.244255 INFO::Writing residuals to file output2/fits/residuals.rds
2025-03-18 21:50:52.321255 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-03-18 21:50:52.388587 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-03-18 21:50:52.394571 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-03-18 21:50:52.400444 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 33.047   0.736  33.993

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin295.886 1.85998.564