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This page was generated on 2025-11-19 10:14 -0500 (Wed, 19 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4827
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4600
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4564
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 1152/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.3.0  (landing page)
William Nickols
Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: b274055
git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for maaslin3 on kjohnson3

To the developers/maintainers of the maaslin3 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.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: maaslin3
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz
StartedAt: 2025-11-18 20:50:16 -0500 (Tue, 18 Nov 2025)
EndedAt: 2025-11-18 20:55:42 -0500 (Tue, 18 Nov 2025)
EllapsedTime: 326.3 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* 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 ‘maaslin3’ 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 ... OK
* 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
maaslin_plot_results_from_output   16.973  0.802  18.973
maaslin_plot_results               16.906  0.665  20.315
maaslin3                            8.399  0.494   9.478
maaslin_contrast_test               7.812  0.654   9.680
maaslin_write_results_lefse_format  6.018  0.504   6.950
maaslin_write_results               5.625  0.503   6.471
maaslin_fit                         5.082  0.577   6.046
* 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: OK

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.3.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 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(maaslin3)
> 
> test_check("maaslin3")
2025-11-18 20:53:04.764912 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:04.793365 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:04.834187 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:04.843256 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:04.855869 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:04.888212 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:04.890305 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:04.894403 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:04.931118 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:04.933441 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:04.951751 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:04.970632 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:04.97502 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:04.989409 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:05.021302 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:12.243312 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:12.269298 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:12.296113 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:12.304082 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:12.3159 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:12.352458 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:12.354393 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:12.358262 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:12.396488 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:12.39846 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:12.415638 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:12.430425 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:12.43484 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:12.451632 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:12.4786 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:14.548 R[21724:77118459] XType: Using static font registry.
2025-11-18 20:53:22.849221 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:22.879164 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:22.910245 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:22.918773 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:22.930597 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:22.958398 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:22.960428 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:22.965099 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:23.007884 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:23.010037 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:23.027735 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:23.043964 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:23.048473 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:23.063934 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:23.088485 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:28.691979 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:28.735943 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:28.765987 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:28.774797 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:28.786984 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:28.813871 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:28.81595 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:28.820099 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:28.857448 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:28.85958 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:28.878476 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:28.892241 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:28.897288 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:28.912586 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:28.936914 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:29.026456 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/residuals_linear.rds
2025-11-18 20:53:29.060449 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/fitted_linear.rds
2025-11-18 20:53:29.096682 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/residuals_logistic.rds
2025-11-18 20:53:29.285911 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/fitted_logistic.rds
2025-11-18 20:53:38.757604 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:38.796375 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:38.824022 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:38.833683 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:38.848088 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:38.874999 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:38.876929 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:38.881034 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:38.91587 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:38.918384 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:38.93746 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:38.951331 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:38.955489 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:38.969211 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:38.99774 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:44.296499 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:44.326201 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:44.355595 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:44.366624 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:44.379501 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:44.407376 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:44.410089 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:44.414964 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:44.456053 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:44.458703 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:44.479555 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:44.494467 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:44.498772 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:44.512767 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:44.54261 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:44.643552 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/residuals_linear.rds
2025-11-18 20:53:44.677645 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/fitted_linear.rds
2025-11-18 20:53:44.714345 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/residuals_logistic.rds
2025-11-18 20:53:44.918331 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/fitted_logistic.rds
2025-11-18 20:53:54.106356 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:54.136594 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:54.166845 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:54.175264 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:54.195418 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:54.25408 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:54.256728 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:54.261694 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:53:54.295994 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:53:54.298198 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:53:54.316091 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:53:54.331258 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:53:54.335476 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:53:54.351296 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:53:54.376951 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:53:59.838726 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:53:59.867263 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:53:59.902185 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:53:59.910807 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:53:59.927906 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:53:59.954829 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:53:59.957021 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:53:59.961406 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:54:00.001875 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:54:00.003984 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:54:00.023077 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:54:00.042467 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:54:00.04697 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:54:00.063073 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:54:00.09987 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:54:00.190301 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/residuals_linear.rds
2025-11-18 20:54:00.227391 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/fitted_linear.rds
2025-11-18 20:54:00.263078 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/residuals_logistic.rds
2025-11-18 20:54:00.47594 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc1f2d348e/fits/fitted_logistic.rds
2025-11-18 20:54:09.462001 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:54:09.490118 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:54:09.520535 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:54:09.529841 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:54:09.542588 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:54:09.56983 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:54:09.572331 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:54:09.576497 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:54:09.620884 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:54:09.623256 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:54:09.642329 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:54:09.658403 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:54:09.662795 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:54:09.679604 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:54:09.70799 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:54:15.01995 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:54:15.046331 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:54:15.073013 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:54:15.082264 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:54:15.118742 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:54:15.145226 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:54:15.14729 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:54:15.151404 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:54:15.188587 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:54:15.190867 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:54:15.21791 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:54:15.233151 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:54:15.23783 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:54:15.252935 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:54:15.28185 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:54:25.623024 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:54:29.766815 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:54:40.379644 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:54:44.440683 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:54:44.642725 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_linear.rds
2025-11-18 20:54:44.679772 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_linear.rds
2025-11-18 20:54:44.705572 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_logistic.rds
2025-11-18 20:54:44.757122 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_logistic.rds
2025-11-18 20:54:55.165446 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:54:58.104285 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:54:58.244282 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_linear.rds
2025-11-18 20:54:58.278831 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_linear.rds
2025-11-18 20:54:58.302925 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_logistic.rds
2025-11-18 20:54:58.349802 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_logistic.rds
2025-11-18 20:55:06.498788 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:55:09.258774 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 20:55:09.404207 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_linear.rds
2025-11-18 20:55:09.445561 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_linear.rds
2025-11-18 20:55:09.467775 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_logistic.rds
2025-11-18 20:55:09.513663 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_logistic.rds
2025-11-18 20:55:17.424407 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:55:17.452135 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:55:17.483581 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:55:17.508066 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:55:17.522181 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:55:17.550927 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:55:17.553694 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:55:17.559387 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:55:17.597045 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:55:17.599528 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:55:17.617079 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:55:17.636492 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:55:17.640928 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:55:17.658086 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:55:17.684102 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:55:22.928677 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 20:55:22.957425 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 20:55:22.987239 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 20:55:22.995207 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 20:55:23.007311 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 20:55:23.033276 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 20:55:23.035758 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 20:55:23.040943 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 20:55:23.079864 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 20:55:23.082103 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 20:55:23.099541 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 20:55:23.114711 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 20:55:23.119133 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 20:55:23.137221 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 20:55:23.171778 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 20:55:23.28521 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_linear.rds
2025-11-18 20:55:23.320107 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_linear.rds
2025-11-18 20:55:23.358871 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/residuals_logistic.rds
2025-11-18 20:55:23.542534 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc3d8894d5/fits/fitted_logistic.rds
2025-11-18 20:55:32.45218 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-18 20:55:32.459856 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-18 20:55:32.463686 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-18 20:55:32.481714 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-11-18 20:55:32.487569 ERROR::Effect name not found in metadata: d
2025-11-18 20:55:32.491661 ERROR::No user formula provided
2025-11-18 20:55:32.502804 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-18 20:55:32.507746 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-11-18 20:55:33.645067 INFO::Writing function arguments to log file
2025-11-18 20:55:33.651221 INFO::Verifying options selected are valid
2025-11-18 20:55:34.563933 INFO::Writing function arguments to log file
2025-11-18 20:55:34.56879 INFO::Verifying options selected are valid
2025-11-18 20:55:34.569211 INFO::Determining format of input files
2025-11-18 20:55:34.569536 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 20:55:34.570377 INFO::Running selected normalization method: TSS
2025-11-18 20:55:34.570934 INFO::Creating output feature tables folder
2025-11-18 20:55:34.571374 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/features/data_norm.tsv
2025-11-18 20:55:34.571997 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-18 20:55:34.572305 INFO::Total samples in data: 16
2025-11-18 20:55:34.572599 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-18 20:55:34.572882 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-18 20:55:34.573555 INFO::Total filtered features: 0
2025-11-18 20:55:34.573907 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-18 20:55:34.574326 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-18 20:55:34.57466 INFO::Filtered feature names from variance filtering:
2025-11-18 20:55:34.574974 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/features/filtered_data.tsv
2025-11-18 20:55:34.575582 INFO::Running selected transform method: LOG
2025-11-18 20:55:34.576025 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/features/data_transformed.tsv
2025-11-18 20:55:34.576701 INFO::Applying z-score to standardize continuous metadata
2025-11-18 20:55:34.578889 INFO::Running the linear model component
2025-11-18 20:55:34.5843 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:34.585923 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:34.587327 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:34.594958 INFO::Counting total values for each feature
2025-11-18 20:55:34.595744 INFO::Running the logistic model component
2025-11-18 20:55:34.600951 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:34.603057 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:34.609128 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:34.613018 INFO::Counting total values for each feature
2025-11-18 20:55:34.614135 INFO::Re-running abundances for warn_prevalence
2025-11-18 20:55:34.614621 INFO::Running selected normalization method: TSS
2025-11-18 20:55:34.615253 INFO::Running selected transform method: LOG
2025-11-18 20:55:34.62108 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:34.623067 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:34.624726 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:34.657417 INFO::Creating fits folder
2025-11-18 20:55:34.658131 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/fits/residuals_linear.rds
2025-11-18 20:55:34.658662 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/fits/fitted_linear.rds
2025-11-18 20:55:34.659181 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/fits/residuals_logistic.rds
2025-11-18 20:55:34.659702 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/fits/fitted_logistic.rds
2025-11-18 20:55:34.660829 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/all_results.tsv
2025-11-18 20:55:34.661547 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/significant_results.tsv
2025-11-18 20:55:34.662082 INFO::Creating output figures folder
2025-11-18 20:55:34.662605 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/figures/summary_plot.pdf
2025-11-18 20:55:35.324557 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/figures
2025-11-18 20:55:35.325409 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 20:55:35.327431 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 20:55:35.546336 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/figures/summary_plot.pdf
2025-11-18 20:55:36.235316 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc2c0dbac1/figures
2025-11-18 20:55:36.236007 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 20:55:36.238179 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 20:55:36.463468 INFO::Running the linear model component
2025-11-18 20:55:36.466491 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:36.468039 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:36.469256 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:36.471638 INFO::Counting total values for each feature
2025-11-18 20:55:36.47225 INFO::Running the logistic model component
2025-11-18 20:55:36.475008 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:36.477033 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:36.480892 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:36.483621 INFO::Counting total values for each feature
2025-11-18 20:55:36.484271 INFO::Re-running abundances for warn_prevalence
2025-11-18 20:55:36.484504 INFO::Running selected normalization method: TSS
2025-11-18 20:55:36.48492 INFO::Running selected transform method: LOG
2025-11-18 20:55:36.487511 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:36.488726 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:36.489852 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:36.517815 INFO::Creating output folder
2025-11-18 20:55:36.518303 INFO::Creating output figures folder
2025-11-18 20:55:36.518835 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc125d7cc8/figures/summary_plot.pdf
2025-11-18 20:55:37.160694 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc125d7cc8/figures
2025-11-18 20:55:37.161428 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 20:55:37.163616 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 20:55:37.686454 INFO::Applying z-score to standardize continuous metadata
2025-11-18 20:55:37.68944 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-18 20:55:37.689745 INFO::Bypass z-score application to metadata
2025-11-18 20:55:37.690555 INFO::Bypass z-score application to metadata
2025-11-18 20:55:37.698016 INFO::Determining format of input files
2025-11-18 20:55:37.698363 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 20:55:37.698619 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-18 20:55:37.700843 INFO::Determining format of input files
2025-11-18 20:55:37.701165 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-18 20:55:37.701546 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 20:55:37.703959 INFO::Determining format of input files
2025-11-18 20:55:37.704238 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 20:55:37.704534 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 20:55:37.704994 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-18 20:55:37.70521 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-18 20:55:37.708845 INFO::Running selected transform method: LOG
2025-11-18 20:55:37.709188 INFO::Creating output feature tables folder
2025-11-18 20:55:37.70955 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc21ed9d93/features/data_transformed.tsv
2025-11-18 20:55:37.710942 INFO::Running selected transform method: LOG
2025-11-18 20:55:37.711303 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc21ed9d93/features/data_transformed.tsv
2025-11-18 20:55:37.712571 INFO::Running selected transform method: PLOG
2025-11-18 20:55:37.713057 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc21ed9d93/features/data_transformed.tsv
2025-11-18 20:55:37.713958 INFO::Running selected transform method: NONE
2025-11-18 20:55:37.714195 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc21ed9d93/features/data_transformed.tsv
2025-11-18 20:55:37.724365 INFO::Running the linear model component
2025-11-18 20:55:37.727134 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:37.728568 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:37.729794 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:37.732142 INFO::Counting total values for each feature
2025-11-18 20:55:37.732695 INFO::Running the logistic model component
2025-11-18 20:55:37.735271 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:37.737179 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:37.738945 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:37.7417 INFO::Counting total values for each feature
2025-11-18 20:55:37.74243 INFO::Re-running abundances for warn_prevalence
2025-11-18 20:55:37.742675 INFO::Running selected normalization method: TSS
2025-11-18 20:55:37.743112 INFO::Running selected transform method: LOG
2025-11-18 20:55:37.745815 INFO::Fitting model to feature number 1, a
2025-11-18 20:55:37.74711 INFO::Fitting model to feature number 2, b
2025-11-18 20:55:37.748297 INFO::Fitting model to feature number 3, c
2025-11-18 20:55:37.780218 INFO::Creating output folder
2025-11-18 20:55:37.780736 INFO::Creating fits folder
2025-11-18 20:55:37.781105 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc77042f4b/fits/residuals_linear.rds
2025-11-18 20:55:37.781631 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc77042f4b/fits/fitted_linear.rds
2025-11-18 20:55:37.783301 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc77042f4b/fits/residuals_logistic.rds
2025-11-18 20:55:37.783756 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc77042f4b/fits/fitted_logistic.rds
2025-11-18 20:55:37.784833 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc77042f4b/all_results.tsv
2025-11-18 20:55:37.785496 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9Ppuf9/file54dc77042f4b/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
144.502   4.352 158.221

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.3990.4949.478
maaslin_check_arguments0.0650.0020.066
maaslin_check_formula0.0590.0030.062
maaslin_compute_formula0.0600.0030.069
maaslin_contrast_test7.8120.6549.680
maaslin_filter0.2430.0370.360
maaslin_fit5.0820.5776.046
maaslin_log_arguments0.0580.0040.062
maaslin_normalize0.1290.0100.163
maaslin_plot_results16.906 0.66520.315
maaslin_plot_results_from_output16.973 0.80218.973
maaslin_process_metadata0.2460.0230.279
maaslin_read_data0.0540.0030.066
maaslin_reorder_data0.0540.0030.058
maaslin_transform0.2810.0260.346
maaslin_write_results5.6250.5036.471
maaslin_write_results_lefse_format6.0180.5046.950
preprocess_dna_mtx0.0020.0000.002
preprocess_taxa_mtx0.0010.0000.002