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This page was generated on 2025-01-27 12:10 -0500 (Mon, 27 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4395
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: 2025-01-23 13:00 -0500 (Thu, 23 Jan 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 -0500 (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 kjohnson1

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: /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_1.20.0.tar.gz
StartedAt: 2025-01-24 23:40:19 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-24 23:43:09 -0500 (Fri, 24 Jan 2025)
EllapsedTime: 169.9 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* 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 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 90.734  1.706  92.606
* 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-3.20-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/4.4-arm64/Resources/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 1.9.15
Current TMB package version is 1.9.16
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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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"
2025-01-24 23:42:25.23621 INFO::Writing function arguments to log file
2025-01-24 23:42:25.288656 INFO::Verifying options selected are valid
2025-01-24 23:42:25.333827 INFO::Determining format of input files
2025-01-24 23:42:25.336196 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 23:42:25.343266 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-24 23:42:25.34511 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-01-24 23:42:25.347962 INFO::Filter data based on min abundance and min prevalence
2025-01-24 23:42:25.349127 INFO::Total samples in data: 1595
2025-01-24 23:42:25.350022 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-24 23:42:25.355389 INFO::Total filtered features: 0
2025-01-24 23:42:25.357089 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-24 23:42:25.375468 INFO::Total filtered features with variance filtering: 0
2025-01-24 23:42:25.377059 INFO::Filtered feature names from variance filtering:
2025-01-24 23:42:25.37809 INFO::Running selected normalization method: TSS
2025-01-24 23:42:26.723254 INFO::Bypass z-score application to metadata
2025-01-24 23:42:26.725063 INFO::Running selected transform method: AST
2025-01-24 23:42:26.742763 INFO::Running selected analysis method: LM
2025-01-24 23:42:27.351644 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-24 23:42:27.781728 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-24 23:42:27.975349 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-24 23:42:28.148453 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-24 23:42:28.341058 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-24 23:42:28.516868 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-24 23:42:28.696211 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-24 23:42:28.898135 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-24 23:42:29.077789 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-24 23:42:29.243606 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-24 23:42:29.416447 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-24 23:42:29.605505 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-24 23:42:29.772897 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-24 23:42:29.94784 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-24 23:42:30.159742 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-24 23:42:30.334689 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-24 23:42:30.50197 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-24 23:42:30.679722 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-24 23:42:30.87099 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-24 23:42:31.037894 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-24 23:42:31.203615 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-24 23:42:31.407711 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-24 23:42:31.581905 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-24 23:42:31.754103 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-24 23:42:31.939961 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-24 23:42:32.109925 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-24 23:42:32.276451 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-24 23:42:32.455543 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-24 23:42:32.635707 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-24 23:42:32.812594 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-24 23:42:32.976208 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-24 23:42:33.168066 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-24 23:42:33.344859 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-24 23:42:33.520549 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-24 23:42:33.699783 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-24 23:42:33.871983 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-24 23:42:34.046641 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-24 23:42:34.230432 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-24 23:42:34.394105 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-24 23:42:34.555455 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-24 23:42:34.743895 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-24 23:42:34.918219 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-24 23:42:35.104159 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-24 23:42:35.281493 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-24 23:42:35.444004 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-24 23:42:35.615211 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-24 23:42:35.799339 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-24 23:42:35.973866 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-24 23:42:36.148311 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-24 23:42:36.31359 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-24 23:42:36.483024 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-24 23:42:36.663584 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-24 23:42:36.840004 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-24 23:42:37.029598 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-24 23:42:37.193112 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-24 23:42:37.383274 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-24 23:42:37.568226 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-24 23:42:37.730271 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-24 23:42:37.917877 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-24 23:42:38.090076 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-24 23:42:38.260316 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-24 23:42:38.426842 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-24 23:42:38.606867 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-24 23:42:38.778415 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-24 23:42:38.948627 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-24 23:42:39.108646 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-24 23:42:39.284924 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-24 23:42:39.456619 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-24 23:42:39.629277 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-24 23:42:39.822426 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-24 23:42:40.003604 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-24 23:42:40.480663 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-24 23:42:40.650333 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-24 23:42:40.822597 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-24 23:42:41.011069 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-24 23:42:41.186002 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-24 23:42:41.361074 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-24 23:42:41.548167 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-24 23:42:41.73669 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-24 23:42:41.909773 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-24 23:42:42.083831 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-24 23:42:42.253925 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-24 23:42:42.42299 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-24 23:42:42.590519 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-24 23:42:42.755963 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-24 23:42:42.91715 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-24 23:42:43.090514 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-24 23:42:43.304798 INFO::Counting total values for each feature
2025-01-24 23:42:43.357229 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-01-24 23:42:43.503944 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-01-24 23:42:43.677162 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-01-24 23:42:43.849147 INFO::Writing residuals to file output/fits/residuals.rds
2025-01-24 23:42:43.931114 INFO::Writing fitted values to file output/fits/fitted.rds
2025-01-24 23:42:43.975229 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-01-24 23:42:43.984739 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-01-24 23:42:43.994125 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"
2025-01-24 23:42:44.012049 INFO::Writing function arguments to log file
2025-01-24 23:42:44.018777 INFO::Verifying options selected are valid
2025-01-24 23:42:44.019948 INFO::Determining format of input files
2025-01-24 23:42:44.021199 INFO::Input format is data samples as rows and metadata samples as rows
2025-01-24 23:42:44.027423 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-01-24 23:42:44.028785 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-01-24 23:42:44.030744 INFO::Filter data based on min abundance and min prevalence
2025-01-24 23:42:44.031935 INFO::Total samples in data: 1595
2025-01-24 23:42:44.032913 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-01-24 23:42:44.03815 INFO::Total filtered features: 0
2025-01-24 23:42:44.039476 INFO::Filtered feature names from abundance and prevalence filtering:
2025-01-24 23:42:44.048454 INFO::Total filtered features with variance filtering: 0
2025-01-24 23:42:44.049909 INFO::Filtered feature names from variance filtering:
2025-01-24 23:42:44.050793 INFO::Running selected normalization method: NONE
2025-01-24 23:42:44.05163 INFO::Bypass z-score application to metadata
2025-01-24 23:42:44.052462 INFO::Running selected transform method: AST
2025-01-24 23:42:44.078364 INFO::Running selected analysis method: LM
2025-01-24 23:42:44.080544 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-01-24 23:42:44.250387 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-01-24 23:42:44.43439 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-01-24 23:42:44.592497 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-01-24 23:42:44.783765 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-01-24 23:42:44.939916 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-01-24 23:42:45.115084 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-01-24 23:42:45.286419 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-01-24 23:42:45.444157 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-01-24 23:42:45.606435 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-01-24 23:42:45.777825 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-01-24 23:42:45.949835 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-01-24 23:42:46.12442 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-01-24 23:42:46.315156 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-01-24 23:42:46.489237 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-01-24 23:42:46.666209 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-01-24 23:42:46.844206 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-01-24 23:42:46.997792 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-01-24 23:42:47.114354 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-01-24 23:42:47.205756 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-01-24 23:42:47.331296 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-01-24 23:42:47.473 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-01-24 23:42:47.618993 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-01-24 23:42:47.689776 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-01-24 23:42:47.770326 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-01-24 23:42:47.892701 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-01-24 23:42:48.054703 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-01-24 23:42:48.241303 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-01-24 23:42:48.395376 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-01-24 23:42:48.550921 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-01-24 23:42:48.723461 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-01-24 23:42:48.881827 INFO::Fitting model to feature number 32, Prevotella.copri
2025-01-24 23:42:49.064992 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-01-24 23:42:49.225668 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-01-24 23:42:49.38999 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-01-24 23:42:49.561539 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-01-24 23:42:49.725439 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-01-24 23:42:49.899178 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-01-24 23:42:50.060845 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-01-24 23:42:50.222631 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-01-24 23:42:50.377922 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-01-24 23:42:50.567126 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-01-24 23:42:50.729279 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-01-24 23:42:50.907132 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-01-24 23:42:51.338565 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-01-24 23:42:51.499031 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-01-24 23:42:51.665635 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-01-24 23:42:51.825769 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-01-24 23:42:52.0024 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-01-24 23:42:52.161305 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-01-24 23:42:52.310249 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-01-24 23:42:52.484037 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-01-24 23:42:52.636109 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-01-24 23:42:52.78906 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-01-24 23:42:52.947388 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-01-24 23:42:53.115927 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-01-24 23:42:53.276858 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-01-24 23:42:53.436471 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-01-24 23:42:53.607217 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-01-24 23:42:53.768042 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-01-24 23:42:53.921959 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-01-24 23:42:54.092132 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-01-24 23:42:54.256587 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-01-24 23:42:54.421348 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-01-24 23:42:54.59493 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-01-24 23:42:54.757251 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-01-24 23:42:54.915856 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-01-24 23:42:55.092021 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-01-24 23:42:55.250663 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-01-24 23:42:55.42136 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-01-24 23:42:55.606814 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-01-24 23:42:55.768202 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-01-24 23:42:55.826236 WARNING::Fitting problem for feature 72 a warning was issued
2025-01-24 23:42:55.997551 INFO::Fitting model to feature number 73, Dialister.invisus
2025-01-24 23:42:56.168564 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-01-24 23:42:56.327883 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-01-24 23:42:56.496321 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-01-24 23:42:56.660644 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-01-24 23:42:56.819662 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-01-24 23:42:56.99175 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-01-24 23:42:57.164412 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-01-24 23:42:57.331037 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-01-24 23:42:57.499384 INFO::Fitting model to feature number 82, Escherichia.coli
2025-01-24 23:42:57.658936 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-01-24 23:42:57.828759 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-01-24 23:42:57.990725 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-01-24 23:42:58.16622 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-01-24 23:42:58.335077 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-01-24 23:42:58.531612 INFO::Counting total values for each feature
2025-01-24 23:42:58.558514 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-01-24 23:42:58.704713 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-01-24 23:42:58.851088 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-01-24 23:42:59.023574 INFO::Writing residuals to file output2/fits/residuals.rds
2025-01-24 23:42:59.439542 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-01-24 23:42:59.546018 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-01-24 23:42:59.555361 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-01-24 23:42:59.562268 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 1 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 34.891   0.791  35.727

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin290.734 1.70692.606