Back to Build/check report for BioC 3.22:   simplified   long
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This page was generated on 2026-04-08 11:57 -0400 (Wed, 08 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
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 1170/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.2.0  (landing page)
William Nickols
Snapshot Date: 2026-04-07 13:45 -0400 (Tue, 07 Apr 2026)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_22
git_last_commit: 9669f95
git_last_commit_date: 2025-10-29 11:33:46 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for maaslin3 in R Universe.

CHECK results for maaslin3 on nebbiolo2

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: 1.2.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
StartedAt: 2026-04-08 00:55:14 -0400 (Wed, 08 Apr 2026)
EndedAt: 2026-04-08 01:16:56 -0400 (Wed, 08 Apr 2026)
EllapsedTime: 1302.3 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 loading without being on the library search path ... 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   44.228  0.377  44.681
maaslin_plot_results               43.743  0.161  43.865
maaslin3                           19.874  0.467  20.344
maaslin_contrast_test              19.188  0.427  19.616
maaslin_write_results_lefse_format 14.563  0.094  14.667
maaslin_write_results              14.219  0.187  14.406
maaslin_fit                        12.938  0.124  13.064
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.2.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
2026-04-08 01:01:29.638609 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:01:29.725222 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:01:29.818202 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:01:29.839751 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:01:29.874934 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:01:29.951613 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:01:29.963563 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:01:29.975166 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:01:30.067944 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:01:30.073205 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:01:30.122644 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:01:30.189662 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:01:30.201833 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:01:30.241762 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:01:30.309812 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:01:46.023317 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:01:46.095619 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:01:46.167189 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:01:46.188501 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:01:46.222537 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:01:46.311814 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:01:46.317105 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:01:46.328715 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:01:46.423619 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:01:46.428906 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:01:46.476795 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:01:46.515598 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:01:46.52713 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:01:46.565864 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:01:46.633584 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:02:10.941615 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:02:11.016856 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:02:11.090292 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:02:11.111561 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:02:11.145647 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:02:11.221202 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:02:11.226536 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:02:11.238217 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:02:11.334113 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:02:11.339723 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:02:11.389963 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:02:11.429849 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:02:11.442301 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:02:11.486054 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:02:11.556328 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:02:24.377601 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:02:24.483971 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:02:24.56068 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:02:24.583637 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:02:24.619022 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:02:24.70005 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:02:24.70577 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:02:24.718827 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:02:24.817778 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:02:24.823327 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:02:24.875969 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:02:24.919084 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:02:24.931144 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:02:24.973286 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:02:25.042617 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:02:25.241057 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/residuals_linear.rds
2026-04-08 01:02:25.302244 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/fitted_linear.rds
2026-04-08 01:02:25.365167 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/residuals_logistic.rds
2026-04-08 01:02:25.665005 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/fitted_logistic.rds
2026-04-08 01:02:48.222637 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:02:48.302851 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:02:48.404949 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:02:48.428015 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:02:48.464161 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:02:48.542682 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:02:48.548367 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:02:48.560553 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:02:48.657315 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:02:48.662833 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:02:48.713178 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:02:48.754009 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:02:48.765995 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:02:48.806644 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:02:48.878971 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:03:01.025418 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:03:01.104004 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:03:01.18055 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:03:01.203224 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:03:01.238715 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:03:01.316843 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:03:01.322332 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:03:01.33473 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:03:01.436254 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:03:01.442123 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:03:01.497381 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:03:01.542231 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:03:01.555513 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:03:01.598952 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:03:01.688569 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:03:01.910862 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/residuals_linear.rds
2026-04-08 01:03:01.972116 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/fitted_linear.rds
2026-04-08 01:03:02.034721 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/residuals_logistic.rds
2026-04-08 01:03:02.332796 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/fitted_logistic.rds
2026-04-08 01:03:23.75572 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:03:23.844143 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:03:23.927588 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:03:23.952864 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:03:23.991111 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:03:24.111653 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:03:24.11848 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:03:24.132893 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:03:24.236158 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:03:24.242066 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:03:24.296618 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:03:24.340772 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:03:24.35381 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:03:24.395868 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:03:24.470037 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:03:36.694132 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:03:36.775426 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:03:36.853433 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:03:36.876084 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:03:36.9122 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:03:36.991033 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:03:36.996761 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:03:37.009831 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:03:37.11056 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:03:37.116627 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:03:37.172559 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:03:37.214855 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:03:37.227598 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:03:37.268246 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:03:37.33866 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:03:37.542333 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/residuals_linear.rds
2026-04-08 01:03:37.604114 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/fitted_linear.rds
2026-04-08 01:03:37.667032 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/residuals_logistic.rds
2026-04-08 01:03:37.96603 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8139a7fab1/fits/fitted_logistic.rds
2026-04-08 01:03:59.55113 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:03:59.62853 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:03:59.703871 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:03:59.725686 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:03:59.759899 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:03:59.836541 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:03:59.84218 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:03:59.854168 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:03:59.949787 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:03:59.955389 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:04:00.006867 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:04:00.048829 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:04:00.061361 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:04:00.102634 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:04:00.174415 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:04:11.983388 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:04:12.060487 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:04:12.137466 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:04:12.159523 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:04:12.194546 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:04:12.272492 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:04:12.277838 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:04:12.289741 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:04:12.385841 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:04:12.391436 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:04:12.442201 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:04:12.484742 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:04:12.497388 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:04:12.539847 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:04:12.61068 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:04:38.357594 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:04:47.193419 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:05:12.35854 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:05:22.345205 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:05:23.003755 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_linear.rds
2026-04-08 01:05:23.0658 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_linear.rds
2026-04-08 01:05:23.105247 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_logistic.rds
2026-04-08 01:05:23.176581 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_logistic.rds
2026-04-08 01:05:46.10896 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:05:51.474773 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:05:51.788257 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_linear.rds
2026-04-08 01:05:51.849665 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_linear.rds
2026-04-08 01:05:51.888182 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_logistic.rds
2026-04-08 01:05:51.9572 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_logistic.rds
2026-04-08 01:06:10.940441 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:06:17.490378 WARNING::Fitting problem for feature 124 returning NA
2026-04-08 01:06:17.789774 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_linear.rds
2026-04-08 01:06:17.851392 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_linear.rds
2026-04-08 01:06:17.890351 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_logistic.rds
2026-04-08 01:06:17.959428 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_logistic.rds
2026-04-08 01:06:37.445091 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:06:37.525214 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:06:37.603955 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:06:37.62715 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:06:37.664134 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:06:37.745142 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:06:37.750978 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:06:37.787099 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:06:37.896936 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:06:37.902475 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:06:37.955444 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:06:37.998473 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:06:38.01085 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:06:38.053054 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:06:38.125345 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:06:48.850922 WARNING::Fitting problem for feature 50 returning NA
2026-04-08 01:06:48.928852 WARNING::Fitting problem for feature 62 returning NA
2026-04-08 01:06:49.003829 WARNING::Fitting problem for feature 74 returning NA
2026-04-08 01:06:49.025369 WARNING::Fitting problem for feature 78 returning NA
2026-04-08 01:06:49.059446 WARNING::Fitting problem for feature 84 returning NA
2026-04-08 01:06:49.134955 WARNING::Fitting problem for feature 96 returning NA
2026-04-08 01:06:49.140306 WARNING::Fitting problem for feature 97 returning NA
2026-04-08 01:06:49.152174 WARNING::Fitting problem for feature 99 returning NA
2026-04-08 01:06:49.247526 WARNING::Fitting problem for feature 114 returning NA
2026-04-08 01:06:49.252872 WARNING::Fitting problem for feature 115 returning NA
2026-04-08 01:06:49.303518 WARNING::Fitting problem for feature 123 returning NA
2026-04-08 01:06:49.343816 WARNING::Fitting problem for feature 130 returning NA
2026-04-08 01:06:49.355694 WARNING::Fitting problem for feature 132 returning NA
2026-04-08 01:06:49.396242 WARNING::Fitting problem for feature 139 returning NA
2026-04-08 01:06:49.468133 WARNING::Fitting problem for feature 150 returning NA
2026-04-08 01:06:49.760663 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_linear.rds
2026-04-08 01:06:49.821849 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_linear.rds
2026-04-08 01:06:49.884949 WARNING::Deleting existing residuals file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/residuals_logistic.rds
2026-04-08 01:06:50.185705 WARNING::Deleting existing fitted file: /tmp/RtmpPl4HlT/file159d8174db962c/fits/fitted_logistic.rds
2026-04-08 01:07:10.69942 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-04-08 01:07:10.716787 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-04-08 01:07:10.72868 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-04-08 01:07:10.781637 ERROR::No fixed, group, or
                        ordered effects included in formula.
2026-04-08 01:07:10.798807 ERROR::Effect name not found in metadata: d
2026-04-08 01:07:10.81001 ERROR::No user formula provided
2026-04-08 01:07:10.841481 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-04-08 01:07:10.853226 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2026-04-08 01:07:13.749491 INFO::Writing function arguments to log file
2026-04-08 01:07:13.764791 INFO::Verifying options selected are valid
2026-04-08 01:07:16.08934 INFO::Writing function arguments to log file
2026-04-08 01:07:16.101754 INFO::Verifying options selected are valid
2026-04-08 01:07:16.102865 INFO::Determining format of input files
2026-04-08 01:07:16.103865 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-08 01:07:16.106261 INFO::Running selected normalization method: TSS
2026-04-08 01:07:16.107727 INFO::Creating output feature tables folder
2026-04-08 01:07:16.108708 INFO::Writing normalized data to file /tmp/RtmpPl4HlT/file159d815478c0c0/features/data_norm.tsv
2026-04-08 01:07:16.110178 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-04-08 01:07:16.111088 INFO::Total samples in data: 16
2026-04-08 01:07:16.111964 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-04-08 01:07:16.112837 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-04-08 01:07:16.114765 INFO::Total filtered features: 0
2026-04-08 01:07:16.115731 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-04-08 01:07:16.116885 INFO::Total features filtered by non-zero variance filtering: 0
2026-04-08 01:07:16.117838 INFO::Filtered feature names from variance filtering:
2026-04-08 01:07:16.118728 INFO::Writing filtered data to file /tmp/RtmpPl4HlT/file159d815478c0c0/features/filtered_data.tsv
2026-04-08 01:07:16.120184 INFO::Running selected transform method: LOG
2026-04-08 01:07:16.121382 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPl4HlT/file159d815478c0c0/features/data_transformed.tsv
2026-04-08 01:07:16.122993 INFO::Applying z-score to standardize continuous metadata
2026-04-08 01:07:16.127522 INFO::Running the linear model component
2026-04-08 01:07:16.141691 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:16.14632 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:16.150649 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:16.157968 INFO::Counting total values for each feature
2026-04-08 01:07:16.159883 INFO::Running the logistic model component
2026-04-08 01:07:16.173957 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:16.180496 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:16.186697 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:16.195768 INFO::Counting total values for each feature
2026-04-08 01:07:16.198017 INFO::Re-running abundances for warn_prevalence
2026-04-08 01:07:16.198998 INFO::Running selected normalization method: TSS
2026-04-08 01:07:16.200538 INFO::Running selected transform method: LOG
2026-04-08 01:07:16.214751 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:16.21923 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:16.223538 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:16.300241 INFO::Creating fits folder
2026-04-08 01:07:16.301453 INFO::Writing residuals to file /tmp/RtmpPl4HlT/file159d815478c0c0/fits/residuals_linear.rds
2026-04-08 01:07:16.302633 INFO::Writing fitted values to file /tmp/RtmpPl4HlT/file159d815478c0c0/fits/fitted_linear.rds
2026-04-08 01:07:16.303847 INFO::Writing residuals to file /tmp/RtmpPl4HlT/file159d815478c0c0/fits/residuals_logistic.rds
2026-04-08 01:07:16.305042 INFO::Writing fitted values to file /tmp/RtmpPl4HlT/file159d815478c0c0/fits/fitted_logistic.rds
2026-04-08 01:07:16.307438 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpPl4HlT/file159d815478c0c0/all_results.tsv
2026-04-08 01:07:16.309115 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/RtmpPl4HlT/file159d815478c0c0/significant_results.tsv
2026-04-08 01:07:16.310459 INFO::Creating output figures folder
2026-04-08 01:07:16.311823 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpPl4HlT/file159d815478c0c0/figures/summary_plot.pdf
2026-04-08 01:07:17.928243 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpPl4HlT/file159d815478c0c0/figures
2026-04-08 01:07:17.930221 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-08 01:07:17.935282 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-08 01:07:18.455449 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpPl4HlT/file159d815478c0c0/figures/summary_plot.pdf
2026-04-08 01:07:20.112355 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpPl4HlT/file159d815478c0c0/figures
2026-04-08 01:07:20.113883 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-08 01:07:20.118863 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-08 01:07:20.636151 INFO::Running the linear model component
2026-04-08 01:07:20.64497 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:20.649238 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:20.653207 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:20.660004 INFO::Counting total values for each feature
2026-04-08 01:07:20.661626 INFO::Running the logistic model component
2026-04-08 01:07:20.669892 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:20.67608 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:20.681899 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:20.690655 INFO::Counting total values for each feature
2026-04-08 01:07:20.692711 INFO::Re-running abundances for warn_prevalence
2026-04-08 01:07:20.69351 INFO::Running selected normalization method: TSS
2026-04-08 01:07:20.694827 INFO::Running selected transform method: LOG
2026-04-08 01:07:20.703367 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:20.707583 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:20.711622 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:20.787155 INFO::Creating output folder
2026-04-08 01:07:20.788119 INFO::Creating output figures folder
2026-04-08 01:07:20.789363 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpPl4HlT/file159d813abbfa67/figures/summary_plot.pdf
2026-04-08 01:07:22.427266 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpPl4HlT/file159d813abbfa67/figures
2026-04-08 01:07:22.429161 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-08 01:07:22.434418 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-08 01:07:23.404463 INFO::Applying z-score to standardize continuous metadata
2026-04-08 01:07:23.412467 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-04-08 01:07:23.413364 INFO::Bypass z-score application to metadata
2026-04-08 01:07:23.416033 INFO::Bypass z-score application to metadata
2026-04-08 01:07:23.436631 INFO::Determining format of input files
2026-04-08 01:07:23.437665 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-08 01:07:23.438534 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-04-08 01:07:23.446342 INFO::Determining format of input files
2026-04-08 01:07:23.4474 INFO::Input format is data samples as columns and metadata samples as rows
2026-04-08 01:07:23.448712 INFO::Input format is feature_specific_covariate samples as columns
2026-04-08 01:07:23.45696 INFO::Determining format of input files
2026-04-08 01:07:23.457913 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-08 01:07:23.458925 INFO::Input format is feature_specific_covariate samples as columns
2026-04-08 01:07:23.460586 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-04-08 01:07:23.46136 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-04-08 01:07:23.473177 INFO::Running selected transform method: LOG
2026-04-08 01:07:23.474338 INFO::Creating output feature tables folder
2026-04-08 01:07:23.475193 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPl4HlT/file159d816520766e/features/data_transformed.tsv
2026-04-08 01:07:23.479222 INFO::Running selected transform method: LOG
2026-04-08 01:07:23.48026 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPl4HlT/file159d816520766e/features/data_transformed.tsv
2026-04-08 01:07:23.484256 INFO::Running selected transform method: PLOG
2026-04-08 01:07:23.486068 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPl4HlT/file159d816520766e/features/data_transformed.tsv
2026-04-08 01:07:23.489556 INFO::Running selected transform method: NONE
2026-04-08 01:07:23.490319 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpPl4HlT/file159d816520766e/features/data_transformed.tsv
2026-04-08 01:07:23.498015 INFO::Running the linear model component
2026-04-08 01:07:23.506557 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:23.510727 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:23.514726 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:23.521664 INFO::Counting total values for each feature
2026-04-08 01:07:23.523315 INFO::Running the logistic model component
2026-04-08 01:07:23.53176 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:23.538118 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:23.54406 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:23.55284 INFO::Counting total values for each feature
2026-04-08 01:07:23.554882 INFO::Re-running abundances for warn_prevalence
2026-04-08 01:07:23.555683 INFO::Running selected normalization method: TSS
2026-04-08 01:07:23.557042 INFO::Running selected transform method: LOG
2026-04-08 01:07:23.56563 INFO::Fitting model to feature number 1, a
2026-04-08 01:07:23.569824 INFO::Fitting model to feature number 2, b
2026-04-08 01:07:23.573735 INFO::Fitting model to feature number 3, c
2026-04-08 01:07:23.649988 INFO::Creating output folder
2026-04-08 01:07:23.651011 INFO::Creating fits folder
2026-04-08 01:07:23.651877 INFO::Writing residuals to file /tmp/RtmpPl4HlT/file159d81551b5fd6/fits/residuals_linear.rds
2026-04-08 01:07:23.652869 INFO::Writing fitted values to file /tmp/RtmpPl4HlT/file159d81551b5fd6/fits/fitted_linear.rds
2026-04-08 01:07:23.653928 INFO::Writing residuals to file /tmp/RtmpPl4HlT/file159d81551b5fd6/fits/residuals_logistic.rds
2026-04-08 01:07:23.654965 INFO::Writing fitted values to file /tmp/RtmpPl4HlT/file159d81551b5fd6/fits/fitted_logistic.rds
2026-04-08 01:07:23.657268 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpPl4HlT/file159d81551b5fd6/all_results.tsv
2026-04-08 01:07:23.658762 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/RtmpPl4HlT/file159d81551b5fd6/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
359.861   5.104 364.963

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin319.874 0.46720.344
maaslin_check_arguments0.1430.0000.143
maaslin_check_formula0.1600.0010.161
maaslin_compute_formula0.1480.0020.151
maaslin_contrast_test19.188 0.42719.616
maaslin_filter0.4340.0090.444
maaslin_fit12.938 0.12413.064
maaslin_log_arguments0.1260.0030.129
maaslin_normalize0.2570.0040.262
maaslin_plot_results43.743 0.16143.865
maaslin_plot_results_from_output44.228 0.37744.681
maaslin_process_metadata0.4450.0220.467
maaslin_read_data0.1200.0060.127
maaslin_reorder_data0.1300.0040.134
maaslin_transform0.5570.0240.581
maaslin_write_results14.219 0.18714.406
maaslin_write_results_lefse_format14.563 0.09414.667
preprocess_dna_mtx0.0040.0000.004
preprocess_taxa_mtx0.0040.0000.004