Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
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 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 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    NA    NA  

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: 1.1.2
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: 2025-10-24 22:11:09 -0400 (Fri, 24 Oct 2025)
EndedAt: 2025-10-24 22:25:50 -0400 (Fri, 24 Oct 2025)
EllapsedTime: 881.5 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: 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 ‘1.1.2’
* 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   50.973  1.249  52.779
maaslin_plot_results               50.980  1.068  52.821
maaslin3                           23.263  1.184  32.363
maaslin_contrast_test              21.696  1.241  24.406
maaslin_write_results_lefse_format 17.182  0.797  18.061
maaslin_write_results              15.959  0.556  16.679
maaslin_fit                        14.083  0.772  15.622
* 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 ‘1.1.2’
** 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: 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")
2025-10-24 22:18:59.936548 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:19:00.033104 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:19:00.152196 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:19:00.179203 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:19:00.2233 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:19:00.315905 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:19:00.322648 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:19:00.336498 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:19:00.463203 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:19:00.471514 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:19:00.535107 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:19:00.580705 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:19:00.597119 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:19:00.663866 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:19:00.754948 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:19:18.352233 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:19:18.448737 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:19:18.541396 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:19:18.566522 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:19:18.609491 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:19:18.706821 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:19:18.713735 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:19:18.729726 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:19:18.853305 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:19:18.859992 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:19:18.947969 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:19:18.988816 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:19:19.00122 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:19:19.04624 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:19:19.122813 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:19:23.496 R[27348:640824756] XType: com.apple.fonts is not accessible.
2025-10-24 22:19:23.496 R[27348:640824756] XType: XTFontStaticRegistry is enabled.
2025-10-24 22:19:46.202496 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:19:46.301931 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:19:46.415822 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:19:46.447235 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:19:46.500689 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:19:46.61732 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:19:46.627259 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:19:46.649863 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:19:46.806374 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:19:46.812778 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:19:46.886379 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:19:46.936977 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:19:46.952611 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:19:47.030064 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:19:47.121303 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:20:02.448622 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:20:02.553638 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:20:02.649668 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:20:02.681375 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:20:02.727014 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:20:02.819035 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:20:02.825323 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:20:02.838868 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:20:02.98975 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:20:02.996195 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:20:03.055686 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:20:03.108409 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:20:03.12277 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:20:03.17783 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:20:03.267411 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:20:03.513818 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad47e635074/fits/residuals_linear.rds
2025-10-24 22:20:03.582947 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad47e635074/fits/fitted_linear.rds
2025-10-24 22:20:03.65569 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad47e635074/fits/residuals_logistic.rds
2025-10-24 22:20:04.003193 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad47e635074/fits/fitted_logistic.rds
2025-10-24 22:20:29.237269 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:20:29.335501 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:20:29.416619 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:20:29.440534 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:20:29.47746 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:20:29.560968 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:20:29.568284 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:20:29.583864 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:20:29.68153 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:20:29.687599 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:20:29.747136 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:20:29.795022 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:20:29.811661 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:20:29.865137 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:20:29.948413 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:20:43.512001 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:20:43.609356 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:20:43.701763 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:20:43.726387 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:20:43.770589 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:20:43.868247 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:20:43.875514 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:20:43.889816 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:20:44.051458 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:20:44.059016 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:20:44.128082 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:20:44.179672 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:20:44.191977 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:20:44.248772 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:20:44.323975 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:20:44.554573 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad47e635074/fits/residuals_linear.rds
2025-10-24 22:20:44.619928 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad47e635074/fits/fitted_linear.rds
2025-10-24 22:20:44.690628 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad47e635074/fits/residuals_logistic.rds
2025-10-24 22:20:45.027854 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad47e635074/fits/fitted_logistic.rds
2025-10-24 22:21:09.171415 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:21:09.276689 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:21:09.369818 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:21:09.393188 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:21:09.430995 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:21:09.532758 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:21:09.538807 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:21:09.554301 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:21:09.691564 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:21:09.700116 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:21:09.768887 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:21:09.819448 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:21:09.832927 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:21:09.883952 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:21:09.965355 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:21:23.665507 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:21:23.751209 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:21:23.847157 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:21:23.878679 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:21:23.929844 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:21:24.02372 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:21:24.031338 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:21:24.049316 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:21:24.22098 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:21:24.227762 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:21:24.284213 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:21:24.331066 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:21:24.344001 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:21:24.389713 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:21:24.474862 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:21:24.703517 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad47e635074/fits/residuals_linear.rds
2025-10-24 22:21:24.772245 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad47e635074/fits/fitted_linear.rds
2025-10-24 22:21:24.843926 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad47e635074/fits/residuals_logistic.rds
2025-10-24 22:21:25.190745 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad47e635074/fits/fitted_logistic.rds
2025-10-24 22:21:48.864635 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:21:48.966357 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:21:49.067715 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:21:49.09864 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:21:49.138464 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:21:49.225564 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:21:49.232939 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:21:49.245628 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:21:49.364528 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:21:49.372661 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:21:49.469819 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:21:49.522145 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:21:49.537161 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:21:49.591577 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:21:49.688872 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:22:03.270672 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:22:03.367176 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:22:03.469994 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:22:03.50627 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:22:03.560156 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:22:03.710783 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:22:03.717955 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:22:03.731288 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:22:03.846524 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:22:03.851776 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:22:03.916387 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:22:03.968846 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:22:03.983656 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:22:04.037096 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:22:04.129271 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:22:30.886242 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:22:41.579531 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:23:08.965166 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:23:20.954235 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:23:21.665827 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_linear.rds
2025-10-24 22:23:21.737929 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_linear.rds
2025-10-24 22:23:21.781176 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_logistic.rds
2025-10-24 22:23:21.854146 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_logistic.rds
2025-10-24 22:23:47.117698 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:23:54.396149 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:23:54.770947 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_linear.rds
2025-10-24 22:23:54.843051 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_linear.rds
2025-10-24 22:23:54.880953 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_logistic.rds
2025-10-24 22:23:54.951073 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_logistic.rds
2025-10-24 22:24:17.82508 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:24:25.179914 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 22:24:25.589248 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_linear.rds
2025-10-24 22:24:25.659477 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_linear.rds
2025-10-24 22:24:25.699202 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_logistic.rds
2025-10-24 22:24:25.780904 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_logistic.rds
2025-10-24 22:24:45.504263 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:24:45.594222 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:24:45.672226 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:24:45.698137 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:24:45.736649 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:24:45.814464 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:24:45.822613 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:24:45.838276 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:24:45.950262 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:24:45.958665 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:24:46.01999 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:24:46.065086 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:24:46.080541 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:24:46.133925 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:24:46.209168 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:24:59.394329 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 22:24:59.490097 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 22:24:59.592013 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 22:24:59.618196 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 22:24:59.656606 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 22:24:59.771684 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 22:24:59.779797 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 22:24:59.797374 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 22:24:59.953883 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 22:24:59.963632 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 22:25:00.045433 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 22:25:00.104844 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 22:25:00.122795 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 22:25:00.174062 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 22:25:00.266889 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 22:25:00.64174 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_linear.rds
2025-10-24 22:25:00.714958 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_linear.rds
2025-10-24 22:25:00.787604 WARNING::Deleting existing residuals file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/residuals_logistic.rds
2025-10-24 22:25:01.13245 WARNING::Deleting existing fitted file: /tmp/RtmpgCaesX/file6ad4aa25e92/fits/fitted_logistic.rds
2025-10-24 22:25:24.656917 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-24 22:25:24.682223 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-24 22:25:24.697248 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-24 22:25:24.771844 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-24 22:25:24.791491 ERROR::Effect name not found in metadata: d
2025-10-24 22:25:24.807338 ERROR::No user formula provided
2025-10-24 22:25:24.846232 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-24 22:25:24.861377 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-24 22:25:28.364955 INFO::Writing function arguments to log file
2025-10-24 22:25:28.390459 INFO::Verifying options selected are valid
2025-10-24 22:25:31.053064 INFO::Writing function arguments to log file
2025-10-24 22:25:31.075192 INFO::Verifying options selected are valid
2025-10-24 22:25:31.076888 INFO::Determining format of input files
2025-10-24 22:25:31.077987 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 22:25:31.081042 INFO::Running selected normalization method: TSS
2025-10-24 22:25:31.082627 INFO::Creating output feature tables folder
2025-10-24 22:25:31.083785 INFO::Writing normalized data to file /tmp/RtmpgCaesX/file6ad46faad9ec/features/data_norm.tsv
2025-10-24 22:25:31.085497 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-24 22:25:31.086855 INFO::Total samples in data: 16
2025-10-24 22:25:31.087864 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-24 22:25:31.088827 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-24 22:25:31.091148 INFO::Total filtered features: 0
2025-10-24 22:25:31.092343 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-24 22:25:31.094059 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-24 22:25:31.095067 INFO::Filtered feature names from variance filtering:
2025-10-24 22:25:31.096106 INFO::Writing filtered data to file /tmp/RtmpgCaesX/file6ad46faad9ec/features/filtered_data.tsv
2025-10-24 22:25:31.098296 INFO::Running selected transform method: LOG
2025-10-24 22:25:31.100167 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgCaesX/file6ad46faad9ec/features/data_transformed.tsv
2025-10-24 22:25:31.10216 INFO::Applying z-score to standardize continuous metadata
2025-10-24 22:25:31.107423 INFO::Running the linear model component
2025-10-24 22:25:31.127882 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:31.132427 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:31.13637 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:31.145231 INFO::Counting total values for each feature
2025-10-24 22:25:31.148212 INFO::Running the logistic model component
2025-10-24 22:25:31.171876 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:31.178852 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:31.185079 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:31.193827 INFO::Counting total values for each feature
2025-10-24 22:25:31.196088 INFO::Re-running abundances for warn_prevalence
2025-10-24 22:25:31.197327 INFO::Running selected normalization method: TSS
2025-10-24 22:25:31.199637 INFO::Running selected transform method: LOG
2025-10-24 22:25:31.219433 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:31.223955 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:31.228676 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:31.323991 INFO::Creating fits folder
2025-10-24 22:25:31.325472 INFO::Writing residuals to file /tmp/RtmpgCaesX/file6ad46faad9ec/fits/residuals_linear.rds
2025-10-24 22:25:31.32695 INFO::Writing fitted values to file /tmp/RtmpgCaesX/file6ad46faad9ec/fits/fitted_linear.rds
2025-10-24 22:25:31.32833 INFO::Writing residuals to file /tmp/RtmpgCaesX/file6ad46faad9ec/fits/residuals_logistic.rds
2025-10-24 22:25:31.329916 INFO::Writing fitted values to file /tmp/RtmpgCaesX/file6ad46faad9ec/fits/fitted_logistic.rds
2025-10-24 22:25:31.333491 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpgCaesX/file6ad46faad9ec/all_results.tsv
2025-10-24 22:25:31.33614 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/RtmpgCaesX/file6ad46faad9ec/significant_results.tsv
2025-10-24 22:25:31.337773 INFO::Creating output figures folder
2025-10-24 22:25:31.339502 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpgCaesX/file6ad46faad9ec/figures/summary_plot.pdf
2025-10-24 22:25:33.194511 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgCaesX/file6ad46faad9ec/figures
2025-10-24 22:25:33.197259 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 22:25:33.205154 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 22:25:33.813666 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpgCaesX/file6ad46faad9ec/figures/summary_plot.pdf
2025-10-24 22:25:35.705463 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgCaesX/file6ad46faad9ec/figures
2025-10-24 22:25:35.706865 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 22:25:35.713394 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 22:25:36.301427 INFO::Running the linear model component
2025-10-24 22:25:36.311961 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:36.317162 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:36.322536 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:36.331609 INFO::Counting total values for each feature
2025-10-24 22:25:36.333831 INFO::Running the logistic model component
2025-10-24 22:25:36.342936 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:36.351783 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:36.358724 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:36.370136 INFO::Counting total values for each feature
2025-10-24 22:25:36.373026 INFO::Re-running abundances for warn_prevalence
2025-10-24 22:25:36.374181 INFO::Running selected normalization method: TSS
2025-10-24 22:25:36.376213 INFO::Running selected transform method: LOG
2025-10-24 22:25:36.385706 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:36.391823 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:36.396908 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:36.511881 INFO::Creating output folder
2025-10-24 22:25:36.513394 INFO::Creating output figures folder
2025-10-24 22:25:36.515338 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpgCaesX/file6ad4e51a98c/figures/summary_plot.pdf
2025-10-24 22:25:38.370785 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgCaesX/file6ad4e51a98c/figures
2025-10-24 22:25:38.372985 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 22:25:38.379973 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 22:25:39.610834 INFO::Applying z-score to standardize continuous metadata
2025-10-24 22:25:39.621365 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-24 22:25:39.622643 INFO::Bypass z-score application to metadata
2025-10-24 22:25:39.626121 INFO::Bypass z-score application to metadata
2025-10-24 22:25:39.652619 INFO::Determining format of input files
2025-10-24 22:25:39.653528 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 22:25:39.654491 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-24 22:25:39.662996 INFO::Determining format of input files
2025-10-24 22:25:39.664787 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-24 22:25:39.667448 INFO::Input format is feature_specific_covariate samples as columns
2025-10-24 22:25:39.67856 INFO::Determining format of input files
2025-10-24 22:25:39.679646 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 22:25:39.681083 INFO::Input format is feature_specific_covariate samples as columns
2025-10-24 22:25:39.683546 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-24 22:25:39.684372 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-24 22:25:39.700755 INFO::Running selected transform method: LOG
2025-10-24 22:25:39.702333 INFO::Creating output feature tables folder
2025-10-24 22:25:39.703823 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgCaesX/file6ad43f0892eb/features/data_transformed.tsv
2025-10-24 22:25:39.709835 INFO::Running selected transform method: LOG
2025-10-24 22:25:39.711521 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgCaesX/file6ad43f0892eb/features/data_transformed.tsv
2025-10-24 22:25:39.717187 INFO::Running selected transform method: PLOG
2025-10-24 22:25:39.719458 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgCaesX/file6ad43f0892eb/features/data_transformed.tsv
2025-10-24 22:25:39.724165 INFO::Running selected transform method: NONE
2025-10-24 22:25:39.724982 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgCaesX/file6ad43f0892eb/features/data_transformed.tsv
2025-10-24 22:25:39.734314 INFO::Running the linear model component
2025-10-24 22:25:39.743925 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:39.74811 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:39.752939 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:39.762334 INFO::Counting total values for each feature
2025-10-24 22:25:39.765985 INFO::Running the logistic model component
2025-10-24 22:25:39.779825 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:39.786913 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:39.793916 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:39.803942 INFO::Counting total values for each feature
2025-10-24 22:25:39.805933 INFO::Re-running abundances for warn_prevalence
2025-10-24 22:25:39.807287 INFO::Running selected normalization method: TSS
2025-10-24 22:25:39.809395 INFO::Running selected transform method: LOG
2025-10-24 22:25:39.82039 INFO::Fitting model to feature number 1, a
2025-10-24 22:25:39.825748 INFO::Fitting model to feature number 2, b
2025-10-24 22:25:39.831858 INFO::Fitting model to feature number 3, c
2025-10-24 22:25:39.93301 INFO::Creating output folder
2025-10-24 22:25:39.934261 INFO::Creating fits folder
2025-10-24 22:25:39.935915 INFO::Writing residuals to file /tmp/RtmpgCaesX/file6ad44be5a2a1/fits/residuals_linear.rds
2025-10-24 22:25:39.937831 INFO::Writing fitted values to file /tmp/RtmpgCaesX/file6ad44be5a2a1/fits/fitted_linear.rds
2025-10-24 22:25:39.939339 INFO::Writing residuals to file /tmp/RtmpgCaesX/file6ad44be5a2a1/fits/residuals_logistic.rds
2025-10-24 22:25:39.940644 INFO::Writing fitted values to file /tmp/RtmpgCaesX/file6ad44be5a2a1/fits/fitted_logistic.rds
2025-10-24 22:25:39.944612 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpgCaesX/file6ad44be5a2a1/all_results.tsv
2025-10-24 22:25:39.947517 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/RtmpgCaesX/file6ad44be5a2a1/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
402.605   7.930 412.975

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin323.263 1.18432.363
maaslin_check_arguments0.1940.0050.204
maaslin_check_formula0.2300.0140.288
maaslin_compute_formula0.2110.0130.264
maaslin_contrast_test21.696 1.24124.406
maaslin_filter1.2700.1551.473
maaslin_fit14.083 0.77215.622
maaslin_log_arguments0.1740.0090.194
maaslin_normalize0.4110.0450.578
maaslin_plot_results50.980 1.06852.821
maaslin_plot_results_from_output50.973 1.24952.779
maaslin_process_metadata0.6260.0410.673
maaslin_read_data0.1700.0090.180
maaslin_reorder_data0.1760.0100.188
maaslin_transform0.8680.0790.958
maaslin_write_results15.959 0.55616.679
maaslin_write_results_lefse_format17.182 0.79718.061
preprocess_dna_mtx0.0050.0010.005
preprocess_taxa_mtx0.0040.0010.004