Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:41 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1155/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.0.0  (landing page)
William Nickols
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_21
git_last_commit: 7584c46
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on kjohnson1

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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2025-08-20 01:46:50 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 02:00:25 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 815.3 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.0.0’
* 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               44.246  1.938  46.459
maaslin_plot_results_from_output   43.343  1.476  45.102
maaslin3                           25.025  1.221  26.585
maaslin_contrast_test              21.675  1.567  23.800
maaslin_write_results_lefse_format 17.241  1.058  18.431
maaslin_write_results              16.604  1.163  17.958
maaslin_fit                        15.108  0.786  16.143
* 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/4.5-arm64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.0.0’
** 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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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")
2025-08-20 01:53:53.804491 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:53:53.902044 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:53:53.997603 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:53:54.035288 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:53:54.074041 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:53:54.160224 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:53:54.166863 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:53:54.180133 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:53:54.29707 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:53:54.303607 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:53:54.362844 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:53:54.439334 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:53:54.453136 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:53:54.495929 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:53:54.571235 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:54:15.013786 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:54:15.098049 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:54:15.183094 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:54:15.233853 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:54:15.272049 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:54:15.362166 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:54:15.36937 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:54:15.383564 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:54:15.491789 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:54:15.49817 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:54:15.552324 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:54:15.597007 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:54:15.611089 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:54:15.658426 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:54:15.740295 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:54:19.679 R[5681:313205961] XType: Using static font registry.
2025-08-20 01:54:40.037214 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:54:40.134085 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:54:40.222722 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:54:40.250271 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:54:40.291841 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:54:40.389936 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:54:40.397405 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:54:40.412454 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:54:40.536742 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:54:40.543785 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:54:40.640121 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:54:40.68323 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:54:40.69685 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:54:40.74017 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:54:40.815209 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:54:56.937163 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:54:57.02765 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:54:57.119351 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:54:57.148502 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:54:57.191609 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:54:57.281212 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:54:57.28886 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:54:57.304817 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:54:57.433179 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:54:57.439891 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:54:57.544084 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:54:57.590238 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:54:57.605454 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:54:57.651682 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:54:57.728015 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:54:57.95666 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file1631525ca011/fits/residuals_linear.rds
2025-08-20 01:54:58.05847 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file1631525ca011/fits/fitted_linear.rds
2025-08-20 01:54:58.162061 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file1631525ca011/fits/residuals_logistic.rds
2025-08-20 01:54:58.704582 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file1631525ca011/fits/fitted_logistic.rds
2025-08-20 01:55:19.047327 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:55:19.140192 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:55:19.231832 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:55:19.257712 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:55:19.300688 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:55:19.41064 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:55:19.419308 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:55:19.434372 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:55:19.557159 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:55:19.566642 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:55:19.636071 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:55:19.68874 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:55:19.706238 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:55:19.925876 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:55:20.010939 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:55:35.942269 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:55:36.020981 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:55:36.095128 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:55:36.120082 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:55:36.168034 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:55:36.24149 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:55:36.248723 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:55:36.263543 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:55:36.369647 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:55:36.373715 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:55:36.437746 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:55:36.512404 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:55:36.519518 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:55:36.540241 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:55:36.580332 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:55:36.74329 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file1631525ca011/fits/residuals_linear.rds
2025-08-20 01:55:36.800211 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file1631525ca011/fits/fitted_linear.rds
2025-08-20 01:55:36.857202 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file1631525ca011/fits/residuals_logistic.rds
2025-08-20 01:55:37.355004 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file1631525ca011/fits/fitted_logistic.rds
2025-08-20 01:55:58.19668 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:55:58.322535 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:55:58.415058 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:55:58.441679 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:55:58.484969 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:55:58.57487 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:55:58.581757 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:55:58.596072 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:55:58.716225 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:55:58.723545 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:55:58.78383 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:55:58.833608 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:55:58.849693 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:55:58.90588 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:55:58.987204 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:56:14.116533 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:56:14.199688 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:56:14.281207 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:56:14.305849 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:56:14.344658 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:56:14.426983 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:56:14.433534 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:56:14.447327 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:56:14.558644 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:56:14.565777 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:56:14.624972 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:56:14.677268 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:56:14.692607 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:56:14.738921 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:56:14.826283 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:56:15.075594 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file1631525ca011/fits/residuals_linear.rds
2025-08-20 01:56:15.176082 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file1631525ca011/fits/fitted_linear.rds
2025-08-20 01:56:15.279911 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file1631525ca011/fits/residuals_logistic.rds
2025-08-20 01:56:15.793546 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file1631525ca011/fits/fitted_logistic.rds
2025-08-20 01:56:36.533738 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:56:36.619982 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:56:36.70936 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:56:36.735834 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:56:36.777368 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:56:36.865538 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:56:36.87227 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:56:36.88646 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:56:37.040523 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:56:37.047945 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:56:37.103517 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:56:37.150898 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:56:37.166062 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:56:37.212879 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:56:37.290509 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:56:51.857358 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:56:51.975811 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:56:52.069828 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:56:52.097395 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:56:52.144075 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:56:52.241488 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:56:52.248169 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:56:52.266827 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:56:52.388476 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:56:52.395173 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:56:52.459655 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:56:52.517606 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:56:52.533507 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:56:52.586426 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:56:52.678551 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:57:16.0748 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:57:27.716029 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:57:52.59855 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:58:04.131075 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:58:04.58022 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_linear.rds
2025-08-20 01:58:04.620446 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_linear.rds
2025-08-20 01:58:04.666476 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_logistic.rds
2025-08-20 01:58:04.713607 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_logistic.rds
2025-08-20 01:58:28.451543 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:58:36.399058 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:58:36.764522 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_linear.rds
2025-08-20 01:58:36.866582 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_linear.rds
2025-08-20 01:58:36.934612 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_logistic.rds
2025-08-20 01:58:37.05602 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_logistic.rds
2025-08-20 01:58:55.822168 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:59:04.008829 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 01:59:04.35412 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_linear.rds
2025-08-20 01:59:04.455151 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_linear.rds
2025-08-20 01:59:04.522816 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_logistic.rds
2025-08-20 01:59:04.651245 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_logistic.rds
2025-08-20 01:59:23.15089 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:59:23.245161 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:59:23.339238 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:59:23.369121 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:59:23.412456 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:59:23.509893 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:59:23.516739 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:59:23.530897 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:59:23.655239 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:59:23.664297 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:59:23.727907 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:59:23.778024 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:59:23.794023 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:59:23.844495 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:59:23.928222 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:59:38.228751 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 01:59:38.316488 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 01:59:38.404776 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 01:59:38.430185 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 01:59:38.469537 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 01:59:38.562605 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 01:59:38.569453 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 01:59:38.583118 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 01:59:38.699789 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 01:59:38.707251 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 01:59:38.768585 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 01:59:38.817189 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 01:59:38.832344 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 01:59:38.879156 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 01:59:38.962195 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 01:59:39.256224 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_linear.rds
2025-08-20 01:59:39.356298 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_linear.rds
2025-08-20 01:59:39.460648 WARNING::Deleting existing residuals file: /tmp/RtmpoVHVxq/file163169256760/fits/residuals_logistic.rds
2025-08-20 01:59:39.975214 WARNING::Deleting existing fitted file: /tmp/RtmpoVHVxq/file163169256760/fits/fitted_logistic.rds
2025-08-20 01:59:59.131161 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-20 01:59:59.146779 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-20 01:59:59.158314 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-20 01:59:59.214627 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-20 01:59:59.235398 ERROR::Effect name not found in metadata: d
2025-08-20 01:59:59.249054 ERROR::No user formula provided
2025-08-20 01:59:59.283392 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-20 01:59:59.29725 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-20 02:00:02.414464 INFO::Writing function arguments to log file
2025-08-20 02:00:02.430142 INFO::Verifying options selected are valid
2025-08-20 02:00:04.631552 INFO::Writing function arguments to log file
2025-08-20 02:00:04.645151 INFO::Verifying options selected are valid
2025-08-20 02:00:04.646951 INFO::Determining format of input files
2025-08-20 02:00:04.648133 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-20 02:00:04.650838 INFO::Running selected normalization method: TSS
2025-08-20 02:00:04.652595 INFO::Creating output feature tables folder
2025-08-20 02:00:04.653932 INFO::Writing normalized data to file /tmp/RtmpoVHVxq/file1631a51936a/features/data_norm.tsv
2025-08-20 02:00:04.655896 INFO::Filter data based on min abundance and min prevalence
2025-08-20 02:00:04.656956 INFO::Total samples in data: 16
2025-08-20 02:00:04.65787 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-20 02:00:04.65987 INFO::Total filtered features: 0
2025-08-20 02:00:04.661081 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-20 02:00:04.662411 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-20 02:00:04.663685 INFO::Filtered feature names from variance filtering:
2025-08-20 02:00:04.664813 INFO::Writing filtered data to file /tmp/RtmpoVHVxq/file1631a51936a/features/filtered_data.tsv
2025-08-20 02:00:04.666997 INFO::Running selected transform method: LOG
2025-08-20 02:00:04.668599 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpoVHVxq/file1631a51936a/features/data_transformed.tsv
2025-08-20 02:00:04.670889 INFO::Applying z-score to standardize continuous metadata
2025-08-20 02:00:04.677769 INFO::Running the linear model component
2025-08-20 02:00:04.693523 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:04.698368 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:04.702404 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:04.708893 INFO::Counting total values for each feature
2025-08-20 02:00:04.710894 INFO::Running the logistic model component
2025-08-20 02:00:04.729566 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:04.736605 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:04.742993 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:04.752377 INFO::Counting total values for each feature
2025-08-20 02:00:04.754929 INFO::Re-running abundances for warn_prevalence
2025-08-20 02:00:04.755948 INFO::Running selected normalization method: TSS
2025-08-20 02:00:04.757478 INFO::Running selected transform method: LOG
2025-08-20 02:00:04.772697 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:04.777543 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:04.781984 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:04.871618 INFO::Creating fits folder
2025-08-20 02:00:04.87346 INFO::Writing residuals to file /tmp/RtmpoVHVxq/file1631a51936a/fits/residuals_linear.rds
2025-08-20 02:00:04.875028 INFO::Writing fitted values to file /tmp/RtmpoVHVxq/file1631a51936a/fits/fitted_linear.rds
2025-08-20 02:00:04.876353 INFO::Writing residuals to file /tmp/RtmpoVHVxq/file1631a51936a/fits/residuals_logistic.rds
2025-08-20 02:00:04.877703 INFO::Writing fitted values to file /tmp/RtmpoVHVxq/file1631a51936a/fits/fitted_logistic.rds
2025-08-20 02:00:04.880691 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpoVHVxq/file1631a51936a/all_results.tsv
2025-08-20 02:00:04.882965 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): /tmp/RtmpoVHVxq/file1631a51936a/significant_results.tsv
2025-08-20 02:00:04.884583 INFO::Creating output figures folder
2025-08-20 02:00:04.886096 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpoVHVxq/file1631a51936a/figures/summary_plot.pdf
2025-08-20 02:00:06.371935 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpoVHVxq/file1631a51936a/figures
2025-08-20 02:00:06.374408 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-20 02:00:06.380343 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-20 02:00:06.849623 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpoVHVxq/file1631a51936a/figures/summary_plot.pdf
2025-08-20 02:00:08.365907 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpoVHVxq/file1631a51936a/figures
2025-08-20 02:00:08.367643 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-20 02:00:08.372935 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-20 02:00:08.843775 INFO::Running the linear model component
2025-08-20 02:00:08.852695 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:08.858131 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:08.862321 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:08.870484 INFO::Counting total values for each feature
2025-08-20 02:00:08.872494 INFO::Running the logistic model component
2025-08-20 02:00:08.880654 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:08.887459 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:08.893427 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:08.902675 INFO::Counting total values for each feature
2025-08-20 02:00:08.905 INFO::Re-running abundances for warn_prevalence
2025-08-20 02:00:08.905796 INFO::Running selected normalization method: TSS
2025-08-20 02:00:08.907149 INFO::Running selected transform method: LOG
2025-08-20 02:00:08.915668 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:08.92026 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:08.925044 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:09.015033 INFO::Creating output folder
2025-08-20 02:00:09.016358 INFO::Creating output figures folder
2025-08-20 02:00:09.017609 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpoVHVxq/file163136c329f9/figures/summary_plot.pdf
2025-08-20 02:00:10.520255 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpoVHVxq/file163136c329f9/figures
2025-08-20 02:00:10.522119 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-20 02:00:10.527985 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-20 02:00:11.608996 INFO::Applying z-score to standardize continuous metadata
2025-08-20 02:00:11.617102 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-20 02:00:11.618005 INFO::Bypass z-score application to metadata
2025-08-20 02:00:11.620365 INFO::Bypass z-score application to metadata
2025-08-20 02:00:11.641595 INFO::Determining format of input files
2025-08-20 02:00:11.642747 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-20 02:00:11.64351 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-20 02:00:11.650308 INFO::Determining format of input files
2025-08-20 02:00:11.651452 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-20 02:00:11.652613 INFO::Input format is feature_specific_covariate samples as columns
2025-08-20 02:00:11.659923 INFO::Determining format of input files
2025-08-20 02:00:11.660925 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-20 02:00:11.661862 INFO::Input format is feature_specific_covariate samples as columns
2025-08-20 02:00:11.663243 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-20 02:00:11.663898 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-20 02:00:11.672833 INFO::Running selected transform method: LOG
2025-08-20 02:00:11.674106 INFO::Creating output feature tables folder
2025-08-20 02:00:11.675227 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpoVHVxq/file16311601d485/features/data_transformed.tsv
2025-08-20 02:00:11.679625 INFO::Running selected transform method: LOG
2025-08-20 02:00:11.68076 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpoVHVxq/file16311601d485/features/data_transformed.tsv
2025-08-20 02:00:11.684857 INFO::Running selected transform method: PLOG
2025-08-20 02:00:11.68683 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpoVHVxq/file16311601d485/features/data_transformed.tsv
2025-08-20 02:00:11.690028 INFO::Running selected transform method: NONE
2025-08-20 02:00:11.690771 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpoVHVxq/file16311601d485/features/data_transformed.tsv
2025-08-20 02:00:11.699057 INFO::Running the linear model component
2025-08-20 02:00:11.707352 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:11.713335 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:11.718896 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:11.727762 INFO::Counting total values for each feature
2025-08-20 02:00:11.72963 INFO::Running the logistic model component
2025-08-20 02:00:11.737446 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:11.743922 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:11.749569 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:11.758748 INFO::Counting total values for each feature
2025-08-20 02:00:11.761029 INFO::Re-running abundances for warn_prevalence
2025-08-20 02:00:11.761855 INFO::Running selected normalization method: TSS
2025-08-20 02:00:11.763254 INFO::Running selected transform method: LOG
2025-08-20 02:00:11.771404 INFO::Fitting model to feature number 1, a
2025-08-20 02:00:11.776011 INFO::Fitting model to feature number 2, b
2025-08-20 02:00:11.780008 INFO::Fitting model to feature number 3, c
2025-08-20 02:00:11.866985 INFO::Creating output folder
2025-08-20 02:00:11.868361 INFO::Creating fits folder
2025-08-20 02:00:11.869228 INFO::Writing residuals to file /tmp/RtmpoVHVxq/file16315227730c/fits/residuals_linear.rds
2025-08-20 02:00:11.870548 INFO::Writing fitted values to file /tmp/RtmpoVHVxq/file16315227730c/fits/fitted_linear.rds
2025-08-20 02:00:11.871623 INFO::Writing residuals to file /tmp/RtmpoVHVxq/file16315227730c/fits/residuals_logistic.rds
2025-08-20 02:00:11.872688 INFO::Writing fitted values to file /tmp/RtmpoVHVxq/file16315227730c/fits/fitted_logistic.rds
2025-08-20 02:00:11.875378 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpoVHVxq/file16315227730c/all_results.tsv
2025-08-20 02:00:11.877314 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): /tmp/RtmpoVHVxq/file16315227730c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
378.064  11.758 391.887

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin325.025 1.22126.585
maaslin_check_arguments0.1830.0070.196
maaslin_check_formula0.1760.0070.183
maaslin_compute_formula0.1770.0070.184
maaslin_contrast_test21.675 1.56723.800
maaslin_filter0.6950.0390.744
maaslin_fit15.108 0.78616.143
maaslin_log_arguments0.1800.0080.190
maaslin_normalize0.4010.0240.427
maaslin_plot_results44.246 1.93846.459
maaslin_plot_results_from_output43.343 1.47645.102
maaslin_process_metadata0.6700.0430.739
maaslin_read_data0.1840.0080.193
maaslin_reorder_data0.2230.0100.234
maaslin_transform2.0450.2532.326
maaslin_write_results16.604 1.16317.958
maaslin_write_results_lefse_format17.241 1.05818.431
preprocess_dna_mtx0.0040.0000.005
preprocess_taxa_mtx0.0040.0000.005