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This page was generated on 2025-11-21 11:39 -0500 (Fri, 21 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4829
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4602
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4566
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 1154/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.3.0  (landing page)
William Nickols
Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 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: 2025-11-20 20:43:29 -0500 (Thu, 20 Nov 2025)
EndedAt: 2025-11-20 20:48:52 -0500 (Thu, 20 Nov 2025)
EllapsedTime: 322.3 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   17.341  0.795  19.117
maaslin_plot_results               16.897  0.636  18.831
maaslin3                            8.692  0.499   9.629
maaslin_contrast_test               6.768  0.674   7.950
maaslin_write_results               5.800  0.550   6.727
maaslin_write_results_lefse_format  5.535  0.500   6.523
maaslin_fit                         5.209  0.457   5.987
* 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")
2025-11-20 20:46:14.764846 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:46:14.792726 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:46:14.830677 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:46:14.839099 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:46:14.851365 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:46:14.884908 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:46:14.886888 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:46:14.890836 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:46:14.930387 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:46:14.932531 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:46:14.949183 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:46:14.971305 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:46:14.976369 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:46:14.99253 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:46:15.018234 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:46:22.328932 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:46:22.354794 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:46:22.382172 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:46:22.390485 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:46:22.402927 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:46:22.441229 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:46:22.443304 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:46:22.447419 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:46:22.48154 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:46:22.483767 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:46:22.500853 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:46:22.514107 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:46:22.518229 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:46:22.532772 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:46:22.557366 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:46:24.582 R[1163:105642949] XType: Using static font registry.
2025-11-20 20:46:32.716065 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:46:32.743754 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:46:32.773945 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:46:32.78426 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:46:32.797654 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:46:32.828117 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:46:32.830537 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:46:32.835855 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:46:32.87051 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:46:32.872583 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:46:32.889793 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:46:32.90501 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:46:32.910512 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:46:32.928388 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:46:32.955525 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:46:38.66939 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:46:38.716229 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:46:38.745913 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:46:38.755921 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:46:38.768753 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:46:38.795605 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:46:38.79764 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:46:38.801627 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:46:38.837097 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:46:38.839477 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:46:38.857977 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:46:38.87169 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:46:38.875842 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:46:38.890153 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:46:38.914184 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:46:38.9926 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/residuals_linear.rds
2025-11-20 20:46:39.030171 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/fitted_linear.rds
2025-11-20 20:46:39.065366 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/residuals_logistic.rds
2025-11-20 20:46:39.25143 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/fitted_logistic.rds
2025-11-20 20:46:48.854001 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:46:48.904122 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:46:48.937302 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:46:48.946297 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:46:48.960822 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:46:48.990779 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:46:48.992978 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:46:48.997088 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:46:49.032831 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:46:49.035023 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:46:49.057035 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:46:49.075529 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:46:49.08037 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:46:49.096197 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:46:49.119963 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:46:54.399129 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:46:54.426997 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:46:54.463436 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:46:54.471101 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:46:54.483068 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:46:54.510838 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:46:54.512997 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:46:54.517252 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:46:54.561451 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:46:54.563507 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:46:54.58303 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:46:54.597581 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:46:54.602043 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:46:54.617561 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:46:54.64285 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:46:54.731895 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/residuals_linear.rds
2025-11-20 20:46:54.767504 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/fitted_linear.rds
2025-11-20 20:46:54.810931 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/residuals_logistic.rds
2025-11-20 20:46:54.99751 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/fitted_logistic.rds
2025-11-20 20:47:04.179523 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:47:04.208974 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:47:04.249023 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:47:04.25686 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:47:04.269563 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:47:04.315207 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:47:04.31729 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:47:04.322111 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:47:04.366026 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:47:04.36832 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:47:04.394542 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:47:04.409618 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:47:04.414153 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:47:04.429608 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:47:04.457301 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:47:09.9866 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:47:10.016187 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:47:10.048294 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:47:10.055973 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:47:10.074673 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:47:10.112234 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:47:10.116726 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:47:10.121236 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:47:10.168113 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:47:10.170396 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:47:10.189019 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:47:10.206645 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:47:10.211816 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:47:10.234634 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:47:10.264092 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:47:10.373417 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/residuals_linear.rds
2025-11-20 20:47:10.410346 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/fitted_linear.rds
2025-11-20 20:47:10.473229 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/residuals_logistic.rds
2025-11-20 20:47:10.678362 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b6c127455/fits/fitted_logistic.rds
2025-11-20 20:47:19.646212 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:47:19.679475 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:47:19.71478 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:47:19.722946 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:47:19.735217 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:47:19.763681 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:47:19.766214 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:47:19.771075 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:47:19.821784 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:47:19.824212 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:47:19.841862 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:47:19.856532 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:47:19.861941 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:47:19.883232 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:47:19.913124 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:47:25.162158 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:47:25.19969 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:47:25.227703 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:47:25.237682 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:47:25.269944 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:47:25.299359 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:47:25.301514 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:47:25.306103 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:47:25.344445 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:47:25.34649 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:47:25.36388 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:47:25.385624 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:47:25.390281 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:47:25.40437 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:47:25.433627 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:47:35.621133 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:47:39.706035 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:47:50.149165 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:47:54.1985 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:47:54.401253 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_linear.rds
2025-11-20 20:47:54.438504 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_linear.rds
2025-11-20 20:47:54.460366 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_logistic.rds
2025-11-20 20:47:54.502474 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_logistic.rds
2025-11-20 20:48:04.747513 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:48:07.60576 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:48:07.763418 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_linear.rds
2025-11-20 20:48:07.802095 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_linear.rds
2025-11-20 20:48:07.825052 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_logistic.rds
2025-11-20 20:48:07.87179 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_logistic.rds
2025-11-20 20:48:15.931259 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:48:18.642815 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 20:48:18.773109 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_linear.rds
2025-11-20 20:48:18.811967 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_linear.rds
2025-11-20 20:48:18.835848 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_logistic.rds
2025-11-20 20:48:18.882374 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_logistic.rds
2025-11-20 20:48:26.753244 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:48:26.781985 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:48:26.810142 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:48:26.839228 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:48:26.851769 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:48:26.878847 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:48:26.881369 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:48:26.886464 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:48:26.921833 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:48:26.923819 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:48:26.940748 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:48:26.956273 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:48:26.961574 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:48:26.977128 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:48:27.003009 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:48:32.18874 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 20:48:32.21975 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 20:48:32.247771 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 20:48:32.256139 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 20:48:32.271348 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 20:48:32.308891 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 20:48:32.31107 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 20:48:32.315374 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 20:48:32.350301 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 20:48:32.352483 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 20:48:32.370483 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 20:48:32.387744 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 20:48:32.392567 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 20:48:32.407982 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 20:48:32.434388 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 20:48:32.566901 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_linear.rds
2025-11-20 20:48:32.600976 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_linear.rds
2025-11-20 20:48:32.637326 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/residuals_logistic.rds
2025-11-20 20:48:32.82021 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b34d7dc7f/fits/fitted_logistic.rds
2025-11-20 20:48:41.35656 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-20 20:48:41.362214 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-20 20:48:41.366339 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-20 20:48:41.384503 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-11-20 20:48:41.391402 ERROR::Effect name not found in metadata: d
2025-11-20 20:48:41.396022 ERROR::No user formula provided
2025-11-20 20:48:41.407195 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-20 20:48:41.411258 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-11-20 20:48:42.526941 INFO::Writing function arguments to log file
2025-11-20 20:48:42.533823 INFO::Verifying options selected are valid
2025-11-20 20:48:43.495534 INFO::Writing function arguments to log file
2025-11-20 20:48:43.510718 INFO::Verifying options selected are valid
2025-11-20 20:48:43.511147 INFO::Determining format of input files
2025-11-20 20:48:43.51147 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-20 20:48:43.512308 INFO::Running selected normalization method: TSS
2025-11-20 20:48:43.512865 INFO::Creating output feature tables folder
2025-11-20 20:48:43.513316 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/features/data_norm.tsv
2025-11-20 20:48:43.514023 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-20 20:48:43.514353 INFO::Total samples in data: 16
2025-11-20 20:48:43.514646 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-20 20:48:43.514923 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-20 20:48:43.515591 INFO::Total filtered features: 0
2025-11-20 20:48:43.515922 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-20 20:48:43.51632 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-20 20:48:43.516643 INFO::Filtered feature names from variance filtering:
2025-11-20 20:48:43.516954 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/features/filtered_data.tsv
2025-11-20 20:48:43.517546 INFO::Running selected transform method: LOG
2025-11-20 20:48:43.517952 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/features/data_transformed.tsv
2025-11-20 20:48:43.518857 INFO::Applying z-score to standardize continuous metadata
2025-11-20 20:48:43.521166 INFO::Running the linear model component
2025-11-20 20:48:43.526983 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:43.528645 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:43.530023 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:43.532449 INFO::Counting total values for each feature
2025-11-20 20:48:43.533124 INFO::Running the logistic model component
2025-11-20 20:48:43.538076 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:43.540388 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:43.542381 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:43.545374 INFO::Counting total values for each feature
2025-11-20 20:48:43.546193 INFO::Re-running abundances for warn_prevalence
2025-11-20 20:48:43.546583 INFO::Running selected normalization method: TSS
2025-11-20 20:48:43.547097 INFO::Running selected transform method: LOG
2025-11-20 20:48:43.551909 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:43.558992 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:43.560812 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:43.596273 INFO::Creating fits folder
2025-11-20 20:48:43.596926 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/fits/residuals_linear.rds
2025-11-20 20:48:43.597518 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/fits/fitted_linear.rds
2025-11-20 20:48:43.598058 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/fits/residuals_logistic.rds
2025-11-20 20:48:43.598559 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/fits/fitted_logistic.rds
2025-11-20 20:48:43.599622 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/all_results.tsv
2025-11-20 20:48:43.600332 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//Rtmp2eRPYA/file48b106c73b2/significant_results.tsv
2025-11-20 20:48:43.600924 INFO::Creating output figures folder
2025-11-20 20:48:43.601456 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/figures/summary_plot.pdf
2025-11-20 20:48:44.270766 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/figures
2025-11-20 20:48:44.271603 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-20 20:48:44.273904 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-20 20:48:44.502362 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/figures/summary_plot.pdf
2025-11-20 20:48:45.155876 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b106c73b2/figures
2025-11-20 20:48:45.156582 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-20 20:48:45.158706 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-20 20:48:45.390278 INFO::Running the linear model component
2025-11-20 20:48:45.393779 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:45.395662 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:45.397186 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:45.400243 INFO::Counting total values for each feature
2025-11-20 20:48:45.400839 INFO::Running the logistic model component
2025-11-20 20:48:45.403761 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:45.405988 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:45.40799 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:45.411077 INFO::Counting total values for each feature
2025-11-20 20:48:45.411822 INFO::Re-running abundances for warn_prevalence
2025-11-20 20:48:45.412073 INFO::Running selected normalization method: TSS
2025-11-20 20:48:45.412505 INFO::Running selected transform method: LOG
2025-11-20 20:48:45.415133 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:45.416402 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:45.417536 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:45.444044 INFO::Creating output folder
2025-11-20 20:48:45.445175 INFO::Creating output figures folder
2025-11-20 20:48:45.445759 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b4a5091e2/figures/summary_plot.pdf
2025-11-20 20:48:46.095377 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b4a5091e2/figures
2025-11-20 20:48:46.096054 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-20 20:48:46.098068 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-20 20:48:46.600818 INFO::Applying z-score to standardize continuous metadata
2025-11-20 20:48:46.603714 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-20 20:48:46.604011 INFO::Bypass z-score application to metadata
2025-11-20 20:48:46.604797 INFO::Bypass z-score application to metadata
2025-11-20 20:48:46.612994 INFO::Determining format of input files
2025-11-20 20:48:46.613426 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-20 20:48:46.61376 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-20 20:48:46.616574 INFO::Determining format of input files
2025-11-20 20:48:46.621479 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-20 20:48:46.622059 INFO::Input format is feature_specific_covariate samples as columns
2025-11-20 20:48:46.625064 INFO::Determining format of input files
2025-11-20 20:48:46.625392 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-20 20:48:46.625721 INFO::Input format is feature_specific_covariate samples as columns
2025-11-20 20:48:46.626183 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-20 20:48:46.6264 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-20 20:48:46.63015 INFO::Running selected transform method: LOG
2025-11-20 20:48:46.63049 INFO::Creating output feature tables folder
2025-11-20 20:48:46.630851 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b61049186/features/data_transformed.tsv
2025-11-20 20:48:46.63218 INFO::Running selected transform method: LOG
2025-11-20 20:48:46.632503 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b61049186/features/data_transformed.tsv
2025-11-20 20:48:46.633683 INFO::Running selected transform method: PLOG
2025-11-20 20:48:46.634172 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b61049186/features/data_transformed.tsv
2025-11-20 20:48:46.635068 INFO::Running selected transform method: NONE
2025-11-20 20:48:46.635307 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b61049186/features/data_transformed.tsv
2025-11-20 20:48:46.638545 INFO::Running the linear model component
2025-11-20 20:48:46.641654 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:46.643112 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:46.644351 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:46.646659 INFO::Counting total values for each feature
2025-11-20 20:48:46.647208 INFO::Running the logistic model component
2025-11-20 20:48:46.649836 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:46.651747 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:46.653506 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:46.65615 INFO::Counting total values for each feature
2025-11-20 20:48:46.656807 INFO::Re-running abundances for warn_prevalence
2025-11-20 20:48:46.657047 INFO::Running selected normalization method: TSS
2025-11-20 20:48:46.657487 INFO::Running selected transform method: LOG
2025-11-20 20:48:46.660294 INFO::Fitting model to feature number 1, a
2025-11-20 20:48:46.661597 INFO::Fitting model to feature number 2, b
2025-11-20 20:48:46.662827 INFO::Fitting model to feature number 3, c
2025-11-20 20:48:46.691776 INFO::Creating output folder
2025-11-20 20:48:46.692257 INFO::Creating fits folder
2025-11-20 20:48:46.692601 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b72ee262c/fits/residuals_linear.rds
2025-11-20 20:48:46.693086 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b72ee262c/fits/fitted_linear.rds
2025-11-20 20:48:46.693506 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b72ee262c/fits/residuals_logistic.rds
2025-11-20 20:48:46.693922 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b72ee262c/fits/fitted_logistic.rds
2025-11-20 20:48:46.694958 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2eRPYA/file48b72ee262c/all_results.tsv
2025-11-20 20:48:46.695645 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//Rtmp2eRPYA/file48b72ee262c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
144.595   4.294 157.211

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.6920.4999.629
maaslin_check_arguments0.0670.0020.071
maaslin_check_formula0.0600.0030.064
maaslin_compute_formula0.0790.0050.084
maaslin_contrast_test6.7680.6747.950
maaslin_filter0.2340.0170.262
maaslin_fit5.2090.4575.987
maaslin_log_arguments0.0580.0030.067
maaslin_normalize0.1290.0150.155
maaslin_plot_results16.897 0.63618.831
maaslin_plot_results_from_output17.341 0.79519.117
maaslin_process_metadata0.2370.0220.276
maaslin_read_data0.0550.0040.058
maaslin_reorder_data0.0570.0030.061
maaslin_transform0.2930.0260.326
maaslin_write_results5.8000.5506.727
maaslin_write_results_lefse_format5.5350.5006.523
preprocess_dna_mtx0.0020.0010.002
preprocess_taxa_mtx0.0010.0000.002