Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-10-15 12:06 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4866
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4653
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1161/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-14 13:45 -0400 (Tue, 14 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: e7106d5
git_last_commit_date: 2025-10-12 11:00:51 -0400 (Sun, 12 Oct 2025)
nebbiolo2Linux (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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 1.1.2
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_1.1.2.tar.gz
StartedAt: 2025-10-14 20:51:16 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 20:56:05 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 289.5 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.2’
* 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   16.386  0.586  17.074
maaslin_plot_results               16.156  0.691  16.885
maaslin3                            8.278  0.470   8.774
maaslin_contrast_test               6.867  0.677   7.594
maaslin_write_results               5.551  0.542   6.115
maaslin_fit                         5.272  0.613   5.916
maaslin_write_results_lefse_format  5.357  0.483   5.858
* 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 ‘1.1.2’
** 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 (2025-09-10 r88807) -- "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")
2025-10-14 20:53:43.491083 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:53:43.517349 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:53:43.550721 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:53:43.55802 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:53:43.569137 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:53:43.593854 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:53:43.595791 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:53:43.599881 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:53:43.635948 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:53:43.637865 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:53:43.654507 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:53:43.6677 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:53:43.67162 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:53:43.688258 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:53:43.710166 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:53:50.462358 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:53:50.489429 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:53:50.525876 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:53:50.534061 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:53:50.547312 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:53:50.57385 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:53:50.575749 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:53:50.579662 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:53:50.611444 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:53:50.613376 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:53:50.629902 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:53:50.643299 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:53:50.647296 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:53:50.660499 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:53:50.683197 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:53:52.161 R[21403:463241082] XType: Using static font registry.
2025-10-14 20:54:00.012175 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:00.038701 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:00.065374 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:00.073517 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:00.086403 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:00.11482 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:00.117068 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:00.12138 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:00.15595 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:00.158134 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:00.176726 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:00.191352 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:00.195737 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:00.210203 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:00.235327 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:05.521744 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:05.547744 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:05.573033 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:05.580858 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:05.59285 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:05.61948 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:05.621415 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:05.625505 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:05.657723 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:05.659837 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:05.67949 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:05.693941 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:05.698331 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:05.71273 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:05.740224 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:05.829973 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_linear.rds
2025-10-14 20:54:05.862384 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_linear.rds
2025-10-14 20:54:05.896056 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_logistic.rds
2025-10-14 20:54:06.069754 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_logistic.rds
2025-10-14 20:54:14.305521 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:14.332448 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:14.359326 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:14.36714 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:14.379159 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:14.406151 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:14.408255 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:14.41256 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:14.446186 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:14.448253 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:14.468531 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:14.482838 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:14.977433 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:14.990862 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:15.014278 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:20.012179 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:20.058809 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:20.084572 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:20.09227 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:20.104259 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:20.130478 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:20.13255 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:20.136543 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:20.169533 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:20.171472 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:20.18834 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:20.202424 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:20.20662 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:20.220642 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:20.244955 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:20.320332 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_linear.rds
2025-10-14 20:54:20.352963 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_linear.rds
2025-10-14 20:54:20.386591 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_logistic.rds
2025-10-14 20:54:20.560813 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_logistic.rds
2025-10-14 20:54:28.754512 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:28.781219 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:28.813186 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:28.821669 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:28.834434 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:28.864117 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:28.866718 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:28.870944 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:28.905364 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:28.907552 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:28.926064 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:28.944285 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:28.948793 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:28.962612 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:28.988195 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:34.115835 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:34.141957 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:34.167513 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:34.175202 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:34.187377 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:34.213677 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:34.215677 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:34.219851 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:34.253957 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:34.256043 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:34.273288 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:34.287704 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:34.292156 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:34.30751 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:34.334425 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:34.420598 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_linear.rds
2025-10-14 20:54:34.453163 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_linear.rds
2025-10-14 20:54:34.486856 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/residuals_logistic.rds
2025-10-14 20:54:34.663278 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3ff5ea27/fits/fitted_logistic.rds
2025-10-14 20:54:42.829866 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:42.857218 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:42.884157 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:42.892354 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:42.904434 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:42.931154 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:42.933215 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:42.93739 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:42.971154 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:42.973256 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:42.99064 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:43.027401 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:43.032495 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:43.048029 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:43.074709 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:48.139886 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:54:48.167051 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:54:48.193125 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:54:48.201592 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:54:48.214275 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:54:48.240129 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:54:48.242015 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:54:48.245944 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:54:48.27818 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:54:48.280198 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:54:48.297161 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:54:48.310817 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:54:48.315071 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:54:48.328675 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:54:48.351626 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:54:57.467868 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:01.344276 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:10.667054 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:14.442668 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:14.640829 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds
2025-10-14 20:55:14.674066 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds
2025-10-14 20:55:14.696113 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds
2025-10-14 20:55:14.736923 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds
2025-10-14 20:55:23.549601 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:26.163473 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:26.26654 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds
2025-10-14 20:55:26.300483 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds
2025-10-14 20:55:26.323189 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds
2025-10-14 20:55:26.363419 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds
2025-10-14 20:55:33.684329 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:36.294811 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 20:55:36.394542 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds
2025-10-14 20:55:36.429166 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds
2025-10-14 20:55:36.451411 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds
2025-10-14 20:55:36.49225 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds
2025-10-14 20:55:43.557192 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:55:43.5841 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:55:43.610513 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:55:43.618549 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:55:43.63088 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:55:43.673791 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:55:43.675859 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:55:43.679925 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:55:43.71346 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:55:43.715481 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:55:43.733052 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:55:43.74796 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:55:43.752399 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:55:43.766675 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:55:43.790946 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:55:48.748509 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 20:55:48.775778 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 20:55:48.801754 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 20:55:48.809835 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 20:55:48.822318 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 20:55:48.84939 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 20:55:48.851484 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 20:55:48.855869 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 20:55:48.894346 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 20:55:48.896722 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 20:55:48.917249 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 20:55:48.934796 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 20:55:48.939998 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 20:55:48.982654 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 20:55:49.006605 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 20:55:49.094671 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_linear.rds
2025-10-14 20:55:49.132585 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_linear.rds
2025-10-14 20:55:49.167 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/residuals_logistic.rds
2025-10-14 20:55:49.333534 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b5f2480dd/fits/fitted_logistic.rds
2025-10-14 20:55:57.128938 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-14 20:55:57.134379 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-14 20:55:57.138084 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-14 20:55:57.154703 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-14 20:55:57.160192 ERROR::Effect name not found in metadata: d
2025-10-14 20:55:57.164084 ERROR::No user formula provided
2025-10-14 20:55:57.173989 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-14 20:55:57.177955 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-14 20:55:58.193559 INFO::Writing function arguments to log file
2025-10-14 20:55:58.198741 INFO::Verifying options selected are valid
2025-10-14 20:55:59.166869 INFO::Writing function arguments to log file
2025-10-14 20:55:59.172394 INFO::Verifying options selected are valid
2025-10-14 20:55:59.172801 INFO::Determining format of input files
2025-10-14 20:55:59.17313 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 20:55:59.173969 INFO::Running selected normalization method: TSS
2025-10-14 20:55:59.174516 INFO::Creating output feature tables folder
2025-10-14 20:55:59.174933 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/features/data_norm.tsv
2025-10-14 20:55:59.175543 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-14 20:55:59.175864 INFO::Total samples in data: 16
2025-10-14 20:55:59.176154 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-14 20:55:59.176449 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-14 20:55:59.177103 INFO::Total filtered features: 0
2025-10-14 20:55:59.177453 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-14 20:55:59.177846 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-14 20:55:59.178173 INFO::Filtered feature names from variance filtering:
2025-10-14 20:55:59.178483 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/features/filtered_data.tsv
2025-10-14 20:55:59.179044 INFO::Running selected transform method: LOG
2025-10-14 20:55:59.179462 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/features/data_transformed.tsv
2025-10-14 20:55:59.180081 INFO::Applying z-score to standardize continuous metadata
2025-10-14 20:55:59.182076 INFO::Running the linear model component
2025-10-14 20:55:59.187609 INFO::Fitting model to feature number 1, a
2025-10-14 20:55:59.189226 INFO::Fitting model to feature number 2, b
2025-10-14 20:55:59.190737 INFO::Fitting model to feature number 3, c
2025-10-14 20:55:59.193323 INFO::Counting total values for each feature
2025-10-14 20:55:59.194034 INFO::Running the logistic model component
2025-10-14 20:55:59.204787 INFO::Fitting model to feature number 1, a
2025-10-14 20:55:59.208043 INFO::Fitting model to feature number 2, b
2025-10-14 20:55:59.210925 INFO::Fitting model to feature number 3, c
2025-10-14 20:55:59.214879 INFO::Counting total values for each feature
2025-10-14 20:55:59.215879 INFO::Re-running abundances for warn_prevalence
2025-10-14 20:55:59.216397 INFO::Running selected normalization method: TSS
2025-10-14 20:55:59.217091 INFO::Running selected transform method: LOG
2025-10-14 20:55:59.2233 INFO::Fitting model to feature number 1, a
2025-10-14 20:55:59.225096 INFO::Fitting model to feature number 2, b
2025-10-14 20:55:59.226766 INFO::Fitting model to feature number 3, c
2025-10-14 20:55:59.254727 INFO::Creating fits folder
2025-10-14 20:55:59.255297 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/residuals_linear.rds
2025-10-14 20:55:59.255794 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/fitted_linear.rds
2025-10-14 20:55:59.256252 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/residuals_logistic.rds
2025-10-14 20:55:59.256719 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/fits/fitted_logistic.rds
2025-10-14 20:55:59.257648 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/all_results.tsv
2025-10-14 20:55:59.25833 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//RtmpbDtvhL/file539b6a9e95d9/significant_results.tsv
2025-10-14 20:55:59.258846 INFO::Creating output figures folder
2025-10-14 20:55:59.259324 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures/summary_plot.pdf
2025-10-14 20:55:59.845569 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures
2025-10-14 20:55:59.846323 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 20:55:59.848248 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 20:56:00.042536 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures/summary_plot.pdf
2025-10-14 20:56:00.642897 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b6a9e95d9/figures
2025-10-14 20:56:00.643477 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 20:56:00.645328 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 20:56:00.84297 INFO::Running the linear model component
2025-10-14 20:56:00.845679 INFO::Fitting model to feature number 1, a
2025-10-14 20:56:00.847068 INFO::Fitting model to feature number 2, b
2025-10-14 20:56:00.848238 INFO::Fitting model to feature number 3, c
2025-10-14 20:56:00.850492 INFO::Counting total values for each feature
2025-10-14 20:56:00.851033 INFO::Running the logistic model component
2025-10-14 20:56:00.85353 INFO::Fitting model to feature number 1, a
2025-10-14 20:56:00.855438 INFO::Fitting model to feature number 2, b
2025-10-14 20:56:00.85714 INFO::Fitting model to feature number 3, c
2025-10-14 20:56:00.859778 INFO::Counting total values for each feature
2025-10-14 20:56:00.860411 INFO::Re-running abundances for warn_prevalence
2025-10-14 20:56:00.860639 INFO::Running selected normalization method: TSS
2025-10-14 20:56:00.861033 INFO::Running selected transform method: LOG
2025-10-14 20:56:00.863627 INFO::Fitting model to feature number 1, a
2025-10-14 20:56:00.864881 INFO::Fitting model to feature number 2, b
2025-10-14 20:56:00.866021 INFO::Fitting model to feature number 3, c
2025-10-14 20:56:00.892149 INFO::Creating output folder
2025-10-14 20:56:00.8926 INFO::Creating output figures folder
2025-10-14 20:56:00.893054 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3bc9c008/figures/summary_plot.pdf
2025-10-14 20:56:01.484243 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b3bc9c008/figures
2025-10-14 20:56:01.484929 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 20:56:01.486973 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 20:56:01.884784 INFO::Applying z-score to standardize continuous metadata
2025-10-14 20:56:01.887493 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-14 20:56:01.887772 INFO::Bypass z-score application to metadata
2025-10-14 20:56:01.888513 INFO::Bypass z-score application to metadata
2025-10-14 20:56:01.894719 INFO::Determining format of input files
2025-10-14 20:56:01.895028 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 20:56:01.895275 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-14 20:56:01.897426 INFO::Determining format of input files
2025-10-14 20:56:01.897752 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-14 20:56:01.898134 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 20:56:01.90054 INFO::Determining format of input files
2025-10-14 20:56:01.900832 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 20:56:01.901139 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 20:56:01.901607 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-14 20:56:01.901821 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-14 20:56:01.905341 INFO::Running selected transform method: LOG
2025-10-14 20:56:01.905689 INFO::Creating output feature tables folder
2025-10-14 20:56:01.906052 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv
2025-10-14 20:56:01.907316 INFO::Running selected transform method: LOG
2025-10-14 20:56:01.907628 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv
2025-10-14 20:56:01.908753 INFO::Running selected transform method: PLOG
2025-10-14 20:56:01.909229 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv
2025-10-14 20:56:01.910089 INFO::Running selected transform method: NONE
2025-10-14 20:56:01.910317 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b2dee41fb/features/data_transformed.tsv
2025-10-14 20:56:01.912769 INFO::Running the linear model component
2025-10-14 20:56:01.915394 INFO::Fitting model to feature number 1, a
2025-10-14 20:56:01.916772 INFO::Fitting model to feature number 2, b
2025-10-14 20:56:01.917975 INFO::Fitting model to feature number 3, c
2025-10-14 20:56:01.920226 INFO::Counting total values for each feature
2025-10-14 20:56:01.920744 INFO::Running the logistic model component
2025-10-14 20:56:01.92325 INFO::Fitting model to feature number 1, a
2025-10-14 20:56:01.925155 INFO::Fitting model to feature number 2, b
2025-10-14 20:56:01.926941 INFO::Fitting model to feature number 3, c
2025-10-14 20:56:01.929637 INFO::Counting total values for each feature
2025-10-14 20:56:01.930279 INFO::Re-running abundances for warn_prevalence
2025-10-14 20:56:01.930513 INFO::Running selected normalization method: TSS
2025-10-14 20:56:01.930922 INFO::Running selected transform method: LOG
2025-10-14 20:56:01.933525 INFO::Fitting model to feature number 1, a
2025-10-14 20:56:01.934791 INFO::Fitting model to feature number 2, b
2025-10-14 20:56:01.935972 INFO::Fitting model to feature number 3, c
2025-10-14 20:56:01.962361 INFO::Creating output folder
2025-10-14 20:56:01.962816 INFO::Creating fits folder
2025-10-14 20:56:01.963128 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/residuals_linear.rds
2025-10-14 20:56:01.963592 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/fitted_linear.rds
2025-10-14 20:56:01.963963 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/residuals_logistic.rds
2025-10-14 20:56:01.964339 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/fits/fitted_logistic.rds
2025-10-14 20:56:01.96522 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpbDtvhL/file539b752ddd4b/all_results.tsv
2025-10-14 20:56:01.965814 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//RtmpbDtvhL/file539b752ddd4b/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
137.054   5.106 143.086

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.2780.4708.774
maaslin_check_arguments0.0570.0020.058
maaslin_check_formula0.0600.0030.063
maaslin_compute_formula0.0560.0040.061
maaslin_contrast_test6.8670.6777.594
maaslin_filter0.2220.0230.245
maaslin_fit5.2720.6135.916
maaslin_log_arguments0.0560.0060.061
maaslin_normalize0.1260.0110.138
maaslin_plot_results16.156 0.69116.885
maaslin_plot_results_from_output16.386 0.58617.074
maaslin_process_metadata0.2130.0200.234
maaslin_read_data0.0500.0030.052
maaslin_reorder_data0.0510.0030.054
maaslin_transform0.2640.0250.290
maaslin_write_results5.5510.5426.115
maaslin_write_results_lefse_format5.3570.4835.858
preprocess_dna_mtx0.0010.0010.002
preprocess_taxa_mtx0.0020.0000.001