Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-11 12:05 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1150/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: ed6ae28
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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 lconway

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: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2025-09-10 22:53:05 -0400 (Wed, 10 Sep 2025)
EndedAt: 2025-09-10 23:06:10 -0400 (Wed, 10 Sep 2025)
EllapsedTime: 784.4 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_1.1.0.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: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   43.447  1.068  45.043
maaslin_plot_results               42.040  1.108  43.489
maaslin3                           23.410  1.028  24.657
maaslin_contrast_test              20.772  1.063  22.043
maaslin_write_results              17.244  0.900  18.414
maaslin_write_results_lefse_format 17.016  0.589  17.698
maaslin_fit                        15.910  0.843  16.865
* 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-x86_64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.1.0’
** 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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-09-10 23:00:06.778989 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:00:06.879767 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:00:06.990706 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:00:07.019733 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:00:07.08141 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:00:07.183653 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:00:07.192269 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:00:07.211135 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:00:07.359045 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:00:07.367672 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:00:07.431958 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:00:07.482635 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:00:07.500923 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:00:07.562515 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:00:07.667418 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:00:25.651682 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:00:25.750726 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:00:25.836827 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:00:25.862159 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:00:25.910011 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:00:26.004756 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:00:26.010461 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:00:26.025531 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:00:26.154891 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:00:26.162952 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:00:26.251488 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:00:26.301467 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:00:26.316815 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:00:26.367524 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:00:26.443562 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:00:30.106 R[5236:255426489] XType: com.apple.fonts is not accessible.
2025-09-10 23:00:30.106 R[5236:255426489] XType: XTFontStaticRegistry is enabled.
2025-09-10 23:00:48.231368 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:00:48.326586 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:00:48.433999 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:00:48.46424 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:00:48.505443 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:00:48.602759 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:00:48.610437 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:00:48.627835 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:00:48.790748 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:00:48.799265 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:00:48.85878 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:00:48.911885 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:00:48.928004 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:00:48.974936 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:00:49.07064 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:01:04.896078 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:01:04.984573 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:01:05.073211 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:01:05.099699 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:01:05.146565 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:01:05.248453 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:01:05.255061 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:01:05.267027 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:01:05.401214 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:01:05.409248 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:01:05.476617 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:01:05.534831 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:01:05.551645 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:01:05.611272 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:01:05.726958 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:01:06.027147 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_linear.rds
2025-09-10 23:01:06.091788 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_linear.rds
2025-09-10 23:01:06.167234 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_logistic.rds
2025-09-10 23:01:06.536904 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_logistic.rds
2025-09-10 23:01:26.298998 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:01:26.407357 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:01:26.508376 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:01:26.538273 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:01:26.583104 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:01:26.68883 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:01:26.696886 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:01:26.714407 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:01:26.844852 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:01:26.853427 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:01:26.922752 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:01:26.98194 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:01:26.99846 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:01:27.057762 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:01:27.16696 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:01:42.463133 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:01:42.575639 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:01:42.679289 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:01:42.706312 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:01:42.739926 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:01:42.845578 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:01:42.853953 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:01:42.869406 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:01:42.987157 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:01:42.994471 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:01:43.067031 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:01:43.122895 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:01:43.138842 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:01:43.19397 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:01:43.29243 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:01:43.582963 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_linear.rds
2025-09-10 23:01:43.718294 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_linear.rds
2025-09-10 23:01:43.793854 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_logistic.rds
2025-09-10 23:01:44.145433 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_logistic.rds
2025-09-10 23:02:03.278246 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:02:03.375406 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:02:03.484043 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:02:03.513333 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:02:03.563165 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:02:03.66771 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:02:03.675455 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:02:03.693733 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:02:03.820675 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:02:03.828114 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:02:03.885396 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:02:03.977518 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:02:03.992448 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:02:04.041489 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:02:04.130164 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:02:17.993895 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:02:18.100763 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:02:18.208015 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:02:18.235919 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:02:18.284649 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:02:18.39649 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:02:18.405318 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:02:18.424611 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:02:18.554512 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:02:18.562462 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:02:18.630353 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:02:18.689241 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:02:18.706996 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:02:18.771611 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:02:18.87064 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:02:19.120211 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_linear.rds
2025-09-10 23:02:19.192219 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_linear.rds
2025-09-10 23:02:19.266722 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147433e9929c/fits/residuals_logistic.rds
2025-09-10 23:02:19.618361 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147433e9929c/fits/fitted_logistic.rds
2025-09-10 23:02:38.57046 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:02:38.671678 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:02:38.776765 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:02:38.809121 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:02:38.859639 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:02:38.966907 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:02:38.974763 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:02:38.990089 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:02:39.127696 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:02:39.135428 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:02:39.205234 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:02:39.264681 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:02:39.281161 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:02:39.33429 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:02:39.435022 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:02:53.904354 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:02:54.006104 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:02:54.109123 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:02:54.140189 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:02:54.183446 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:02:54.276205 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:02:54.282407 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:02:54.298066 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:02:54.419918 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:02:54.426812 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:02:54.48317 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:02:54.536612 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:02:54.554733 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:02:54.602152 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:02:54.6854 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:03:16.198707 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:03:27.286238 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:03:49.78866 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:04:00.875101 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:04:01.577348 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds
2025-09-10 23:04:01.648908 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds
2025-09-10 23:04:01.69332 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds
2025-09-10 23:04:01.76912 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds
2025-09-10 23:04:21.853251 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:04:28.930739 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:04:29.247639 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds
2025-09-10 23:04:29.310395 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds
2025-09-10 23:04:29.352395 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds
2025-09-10 23:04:29.425068 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds
2025-09-10 23:04:45.842886 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:04:53.153204 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 23:04:53.555207 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds
2025-09-10 23:04:53.624911 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds
2025-09-10 23:04:53.669981 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds
2025-09-10 23:04:53.749994 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds
2025-09-10 23:05:10.411952 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:05:10.519777 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:05:10.65485 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:05:10.67934 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:05:10.726133 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:05:10.82941 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:05:10.837423 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:05:10.853149 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:05:10.974909 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:05:10.980826 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:05:11.053383 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:05:11.104269 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:05:11.122442 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:05:11.179837 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:05:11.26535 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:05:25.121184 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 23:05:25.216528 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 23:05:25.313283 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 23:05:25.343298 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 23:05:25.394296 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 23:05:25.497205 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 23:05:25.503999 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 23:05:25.518107 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 23:05:25.651665 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 23:05:25.658418 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 23:05:25.724381 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 23:05:25.777028 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 23:05:25.793872 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 23:05:25.850821 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 23:05:25.949632 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 23:05:26.342716 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_linear.rds
2025-09-10 23:05:26.40886 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_linear.rds
2025-09-10 23:05:26.482834 WARNING::Deleting existing residuals file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/residuals_logistic.rds
2025-09-10 23:05:26.840426 WARNING::Deleting existing fitted file: /tmp/RtmpnQgYfL/file147463e36f8d/fits/fitted_logistic.rds
2025-09-10 23:05:43.774256 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-10 23:05:43.790539 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-10 23:05:43.805175 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-10 23:05:43.872955 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-09-10 23:05:43.892062 ERROR::Effect name not found in metadata: d
2025-09-10 23:05:43.909703 ERROR::No user formula provided
2025-09-10 23:05:43.950785 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-10 23:05:43.966253 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-09-10 23:05:47.477194 INFO::Writing function arguments to log file
2025-09-10 23:05:47.501391 INFO::Verifying options selected are valid
2025-09-10 23:05:49.579094 INFO::Writing function arguments to log file
2025-09-10 23:05:49.599077 INFO::Verifying options selected are valid
2025-09-10 23:05:49.601389 INFO::Determining format of input files
2025-09-10 23:05:49.603417 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 23:05:49.607746 INFO::Running selected normalization method: TSS
2025-09-10 23:05:49.609645 INFO::Creating output feature tables folder
2025-09-10 23:05:49.610993 INFO::Writing normalized data to file /tmp/RtmpnQgYfL/file14746ab2aa81/features/data_norm.tsv
2025-09-10 23:05:49.613011 INFO::Filter data based on min abundance and min prevalence
2025-09-10 23:05:49.614801 INFO::Total samples in data: 16
2025-09-10 23:05:49.615975 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-10 23:05:49.618753 INFO::Total filtered features: 0
2025-09-10 23:05:49.620421 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 23:05:49.622275 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-10 23:05:49.623324 INFO::Filtered feature names from variance filtering:
2025-09-10 23:05:49.624446 INFO::Writing filtered data to file /tmp/RtmpnQgYfL/file14746ab2aa81/features/filtered_data.tsv
2025-09-10 23:05:49.626822 INFO::Running selected transform method: LOG
2025-09-10 23:05:49.62834 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14746ab2aa81/features/data_transformed.tsv
2025-09-10 23:05:49.630721 INFO::Applying z-score to standardize continuous metadata
2025-09-10 23:05:49.638083 INFO::Running the linear model component
2025-09-10 23:05:49.660918 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:49.666343 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:49.672158 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:49.682991 INFO::Counting total values for each feature
2025-09-10 23:05:49.6857 INFO::Running the logistic model component
2025-09-10 23:05:49.706331 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:49.713117 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:49.72018 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:49.72955 INFO::Counting total values for each feature
2025-09-10 23:05:49.732798 INFO::Re-running abundances for warn_prevalence
2025-09-10 23:05:49.73459 INFO::Running selected normalization method: TSS
2025-09-10 23:05:49.7372 INFO::Running selected transform method: LOG
2025-09-10 23:05:49.757181 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:49.761707 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:49.765821 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:49.888423 INFO::Creating fits folder
2025-09-10 23:05:49.890475 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/residuals_linear.rds
2025-09-10 23:05:49.892729 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/fitted_linear.rds
2025-09-10 23:05:49.894926 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/residuals_logistic.rds
2025-09-10 23:05:49.897155 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file14746ab2aa81/fits/fitted_logistic.rds
2025-09-10 23:05:49.901191 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpnQgYfL/file14746ab2aa81/all_results.tsv
2025-09-10 23:05:49.903698 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/RtmpnQgYfL/file14746ab2aa81/significant_results.tsv
2025-09-10 23:05:49.905346 INFO::Creating output figures folder
2025-09-10 23:05:49.90769 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpnQgYfL/file14746ab2aa81/figures/summary_plot.pdf
2025-09-10 23:05:51.382715 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpnQgYfL/file14746ab2aa81/figures
2025-09-10 23:05:51.385777 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 23:05:51.393684 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 23:05:52.048574 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpnQgYfL/file14746ab2aa81/figures/summary_plot.pdf
2025-09-10 23:05:53.617649 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpnQgYfL/file14746ab2aa81/figures
2025-09-10 23:05:53.619792 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 23:05:53.625205 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 23:05:54.146801 INFO::Running the linear model component
2025-09-10 23:05:54.160654 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:54.167069 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:54.173647 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:54.180857 INFO::Counting total values for each feature
2025-09-10 23:05:54.182552 INFO::Running the logistic model component
2025-09-10 23:05:54.196005 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:54.205481 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:54.211918 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:54.222856 INFO::Counting total values for each feature
2025-09-10 23:05:54.225673 INFO::Re-running abundances for warn_prevalence
2025-09-10 23:05:54.226883 INFO::Running selected normalization method: TSS
2025-09-10 23:05:54.228851 INFO::Running selected transform method: LOG
2025-09-10 23:05:54.239887 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:54.245775 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:54.251353 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:54.377382 INFO::Creating output folder
2025-09-10 23:05:54.379405 INFO::Creating output figures folder
2025-09-10 23:05:54.381012 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpnQgYfL/file1474ed74ebf/figures/summary_plot.pdf
2025-09-10 23:05:55.928576 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpnQgYfL/file1474ed74ebf/figures
2025-09-10 23:05:55.931093 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 23:05:55.93806 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 23:05:56.988238 INFO::Applying z-score to standardize continuous metadata
2025-09-10 23:05:56.999796 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-10 23:05:57.001057 INFO::Bypass z-score application to metadata
2025-09-10 23:05:57.003665 INFO::Bypass z-score application to metadata
2025-09-10 23:05:57.032682 INFO::Determining format of input files
2025-09-10 23:05:57.033599 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 23:05:57.034363 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-10 23:05:57.044228 INFO::Determining format of input files
2025-09-10 23:05:57.045363 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-10 23:05:57.047169 INFO::Input format is feature_specific_covariate samples as columns
2025-09-10 23:05:57.059339 INFO::Determining format of input files
2025-09-10 23:05:57.060445 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 23:05:57.061457 INFO::Input format is feature_specific_covariate samples as columns
2025-09-10 23:05:57.063517 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-10 23:05:57.064274 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-10 23:05:57.078544 INFO::Running selected transform method: LOG
2025-09-10 23:05:57.080387 INFO::Creating output feature tables folder
2025-09-10 23:05:57.082132 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv
2025-09-10 23:05:57.088899 INFO::Running selected transform method: LOG
2025-09-10 23:05:57.090626 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv
2025-09-10 23:05:57.096738 INFO::Running selected transform method: PLOG
2025-09-10 23:05:57.099339 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv
2025-09-10 23:05:57.104146 INFO::Running selected transform method: NONE
2025-09-10 23:05:57.105075 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpnQgYfL/file14743329dad3/features/data_transformed.tsv
2025-09-10 23:05:57.116259 INFO::Running the linear model component
2025-09-10 23:05:57.127864 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:57.132256 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:57.137348 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:57.145182 INFO::Counting total values for each feature
2025-09-10 23:05:57.147789 INFO::Running the logistic model component
2025-09-10 23:05:57.158792 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:57.16753 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:57.174918 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:57.185916 INFO::Counting total values for each feature
2025-09-10 23:05:57.189283 INFO::Re-running abundances for warn_prevalence
2025-09-10 23:05:57.190596 INFO::Running selected normalization method: TSS
2025-09-10 23:05:57.192228 INFO::Running selected transform method: LOG
2025-09-10 23:05:57.201657 INFO::Fitting model to feature number 1, a
2025-09-10 23:05:57.205893 INFO::Fitting model to feature number 2, b
2025-09-10 23:05:57.209846 INFO::Fitting model to feature number 3, c
2025-09-10 23:05:57.333424 INFO::Creating output folder
2025-09-10 23:05:57.335049 INFO::Creating fits folder
2025-09-10 23:05:57.336666 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/residuals_linear.rds
2025-09-10 23:05:57.338205 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/fitted_linear.rds
2025-09-10 23:05:57.339368 INFO::Writing residuals to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/residuals_logistic.rds
2025-09-10 23:05:57.340658 INFO::Writing fitted values to file /tmp/RtmpnQgYfL/file1474dd6ce3/fits/fitted_logistic.rds
2025-09-10 23:05:57.343994 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpnQgYfL/file1474dd6ce3/all_results.tsv
2025-09-10 23:05:57.346474 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/RtmpnQgYfL/file1474dd6ce3/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
354.515   7.572 364.251 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin323.410 1.02824.657
maaslin_check_arguments0.1810.0030.185
maaslin_check_formula0.1760.0090.187
maaslin_compute_formula0.1700.0110.183
maaslin_contrast_test20.772 1.06322.043
maaslin_filter0.6180.0480.672
maaslin_fit15.910 0.84316.865
maaslin_log_arguments0.1710.0090.181
maaslin_normalize0.3720.0240.399
maaslin_plot_results42.040 1.10843.489
maaslin_plot_results_from_output43.447 1.06845.043
maaslin_process_metadata0.6600.0440.709
maaslin_read_data0.1790.0110.195
maaslin_reorder_data0.1920.0110.204
maaslin_transform0.8420.0730.923
maaslin_write_results17.244 0.90018.414
maaslin_write_results_lefse_format17.016 0.58917.698
preprocess_dna_mtx0.0060.0000.006
preprocess_taxa_mtx0.0060.0000.006