Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-19 12:05 -0400 (Tue, 19 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 1147/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-18 13:45 -0400 (Mon, 18 Aug 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: 2025-08-18 22:12:25 -0400 (Mon, 18 Aug 2025)
EndedAt: 2025-08-18 22:25:14 -0400 (Mon, 18 Aug 2025)
EllapsedTime: 769.4 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 (2025-06-13)
* 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   42.451  1.164  43.906
maaslin_plot_results               41.171  1.017  42.489
maaslin3                           23.715  1.036  25.007
maaslin_contrast_test              19.553  0.978  20.725
maaslin_write_results_lefse_format 18.060  0.675  18.828
maaslin_write_results              16.559  0.685  17.381
maaslin_fit                        14.752  0.784  15.646
* 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 (2025-06-13) -- "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")
2025-08-18 22:19:17.455131 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:19:17.555401 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:19:17.663985 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:19:17.694357 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:19:17.75305 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:19:17.84446 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:19:17.851375 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:19:17.866633 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:19:18.003504 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:19:18.010251 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:19:18.068908 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:19:18.120167 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:19:18.136607 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:19:18.187557 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:19:18.284693 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:19:35.729908 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:19:35.819485 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:19:35.902065 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:19:35.929387 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:19:35.977722 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:19:36.079814 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:19:36.109089 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:19:36.126687 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:19:36.241294 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:19:36.249457 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:19:36.304127 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:19:36.343941 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:19:36.358352 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:19:36.406792 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:19:36.496445 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:19:40.090 R[87757:56753903] XType: com.apple.fonts is not accessible.
2025-08-18 22:19:40.090 R[87757:56753903] XType: XTFontStaticRegistry is enabled.
2025-08-18 22:19:56.979823 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:19:57.113854 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:19:57.217669 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:19:57.247073 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:19:57.292428 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:19:57.40171 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:19:57.407628 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:19:57.424814 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:19:57.555364 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:19:57.562295 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:19:57.684279 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:19:57.743976 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:19:57.761482 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:19:57.820236 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:19:57.916764 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:20:13.642992 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:20:13.746632 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:20:13.841067 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:20:13.871051 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:20:13.919778 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:20:14.022967 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:20:14.03035 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:20:14.048254 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:20:14.183564 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:20:14.191119 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:20:14.261259 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:20:14.316242 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:20:14.332317 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:20:14.389801 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:20:14.483308 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:20:14.748129 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/residuals_linear.rds
2025-08-18 22:20:14.815225 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/fitted_linear.rds
2025-08-18 22:20:14.88425 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/residuals_logistic.rds
2025-08-18 22:20:15.250279 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/fitted_logistic.rds
2025-08-18 22:20:34.568338 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:20:34.673094 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:20:34.778819 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:20:34.804589 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:20:34.855701 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:20:34.943048 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:20:34.950157 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:20:34.968279 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:20:35.0855 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:20:35.09194 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:20:35.151851 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:20:35.200236 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:20:35.216803 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:20:35.276954 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:20:35.374301 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:20:50.424658 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:20:50.529808 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:20:50.628462 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:20:50.652488 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:20:50.697138 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:20:50.806142 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:20:50.813443 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:20:50.830334 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:20:50.950623 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:20:50.959202 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:20:51.025139 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:20:51.081425 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:20:51.096565 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:20:51.159879 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:20:51.262521 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:20:51.525326 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/residuals_linear.rds
2025-08-18 22:20:51.594201 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/fitted_linear.rds
2025-08-18 22:20:51.657392 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/residuals_logistic.rds
2025-08-18 22:20:51.993073 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/fitted_logistic.rds
2025-08-18 22:21:10.850938 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:21:10.945452 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:21:11.038579 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:21:11.070944 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:21:11.116115 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:21:11.21479 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:21:11.220326 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:21:11.234639 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:21:11.356838 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:21:11.363887 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:21:11.428211 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:21:11.480243 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:21:11.496211 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:21:11.602673 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:21:11.692944 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:21:24.84021 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:21:24.937063 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:21:25.018849 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:21:25.044447 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:21:25.139715 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:21:25.229974 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:21:25.23529 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:21:25.248988 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:21:25.361589 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:21:25.367587 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:21:25.430841 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:21:25.479134 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:21:25.49422 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:21:25.539515 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:21:25.624667 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:21:25.860638 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/residuals_linear.rds
2025-08-18 22:21:25.924857 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/fitted_linear.rds
2025-08-18 22:21:25.990706 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/residuals_logistic.rds
2025-08-18 22:21:26.326605 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd2e0b9996/fits/fitted_logistic.rds
2025-08-18 22:21:44.749615 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:21:44.845595 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:21:44.945174 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:21:44.97573 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:21:45.020231 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:21:45.118876 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:21:45.124892 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:21:45.141565 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:21:45.27176 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:21:45.281762 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:21:45.343569 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:21:45.392513 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:21:45.407411 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:21:45.460596 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:21:45.547271 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:21:59.49669 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:21:59.59544 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:21:59.687905 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:21:59.718388 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:21:59.760959 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:21:59.850424 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:21:59.856878 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:21:59.871939 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:21:59.993204 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:22:00.001839 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:22:00.075623 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:22:00.134061 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:22:00.147733 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:22:00.207189 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:22:00.300209 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:22:21.332238 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:22:32.54099 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:22:55.266021 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:23:06.292025 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:23:07.042671 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_linear.rds
2025-08-18 22:23:07.109823 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_linear.rds
2025-08-18 22:23:07.157293 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_logistic.rds
2025-08-18 22:23:07.231743 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_logistic.rds
2025-08-18 22:23:27.448699 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:23:33.48984 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:23:33.834433 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_linear.rds
2025-08-18 22:23:33.904868 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_linear.rds
2025-08-18 22:23:33.950245 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_logistic.rds
2025-08-18 22:23:34.024147 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_logistic.rds
2025-08-18 22:23:51.386321 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:23:57.503261 WARNING::Fitting problem for feature 124 returning NA
2025-08-18 22:23:57.903149 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_linear.rds
2025-08-18 22:23:57.97307 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_linear.rds
2025-08-18 22:23:58.019029 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_logistic.rds
2025-08-18 22:23:58.087509 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_logistic.rds
2025-08-18 22:24:15.180164 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:24:15.261999 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:24:15.353813 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:24:15.378206 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:24:15.42321 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:24:15.51556 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:24:15.522063 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:24:15.540483 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:24:15.66264 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:24:15.671539 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:24:15.743013 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:24:15.805757 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:24:15.820476 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:24:15.880464 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:24:15.965907 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:24:28.398341 WARNING::Fitting problem for feature 50 returning NA
2025-08-18 22:24:28.494506 WARNING::Fitting problem for feature 62 returning NA
2025-08-18 22:24:28.594905 WARNING::Fitting problem for feature 74 returning NA
2025-08-18 22:24:28.625109 WARNING::Fitting problem for feature 78 returning NA
2025-08-18 22:24:28.67121 WARNING::Fitting problem for feature 84 returning NA
2025-08-18 22:24:28.771831 WARNING::Fitting problem for feature 96 returning NA
2025-08-18 22:24:28.779099 WARNING::Fitting problem for feature 97 returning NA
2025-08-18 22:24:28.79593 WARNING::Fitting problem for feature 99 returning NA
2025-08-18 22:24:28.912334 WARNING::Fitting problem for feature 114 returning NA
2025-08-18 22:24:28.919387 WARNING::Fitting problem for feature 115 returning NA
2025-08-18 22:24:28.982693 WARNING::Fitting problem for feature 123 returning NA
2025-08-18 22:24:30.123721 WARNING::Fitting problem for feature 130 returning NA
2025-08-18 22:24:30.135252 WARNING::Fitting problem for feature 132 returning NA
2025-08-18 22:24:30.189219 WARNING::Fitting problem for feature 139 returning NA
2025-08-18 22:24:30.284983 WARNING::Fitting problem for feature 150 returning NA
2025-08-18 22:24:30.594164 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_linear.rds
2025-08-18 22:24:30.667247 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_linear.rds
2025-08-18 22:24:30.740267 WARNING::Deleting existing residuals file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/residuals_logistic.rds
2025-08-18 22:24:31.090411 WARNING::Deleting existing fitted file: /tmp/Rtmpv41tN1/file156cd4f135599/fits/fitted_logistic.rds
2025-08-18 22:24:48.982094 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-18 22:24:49.005635 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-18 22:24:49.024225 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-18 22:24:49.094945 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-18 22:24:49.114256 ERROR::Effect name not found in metadata: d
2025-08-18 22:24:49.126443 ERROR::No user formula provided
2025-08-18 22:24:49.170755 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-18 22:24:49.188637 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-18 22:24:52.624669 INFO::Writing function arguments to log file
2025-08-18 22:24:52.65115 INFO::Verifying options selected are valid
2025-08-18 22:24:54.841212 INFO::Writing function arguments to log file
2025-08-18 22:24:54.86145 INFO::Verifying options selected are valid
2025-08-18 22:24:54.863152 INFO::Determining format of input files
2025-08-18 22:24:54.864566 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-18 22:24:54.868038 INFO::Running selected normalization method: TSS
2025-08-18 22:24:54.869783 INFO::Creating output feature tables folder
2025-08-18 22:24:54.871456 INFO::Writing normalized data to file /tmp/Rtmpv41tN1/file156cd1ab8b775/features/data_norm.tsv
2025-08-18 22:24:54.8739 INFO::Filter data based on min abundance and min prevalence
2025-08-18 22:24:54.875323 INFO::Total samples in data: 16
2025-08-18 22:24:54.876657 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-18 22:24:54.879436 INFO::Total filtered features: 0
2025-08-18 22:24:54.881105 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-18 22:24:54.882344 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-18 22:24:54.883329 INFO::Filtered feature names from variance filtering:
2025-08-18 22:24:54.884256 INFO::Writing filtered data to file /tmp/Rtmpv41tN1/file156cd1ab8b775/features/filtered_data.tsv
2025-08-18 22:24:54.886484 INFO::Running selected transform method: LOG
2025-08-18 22:24:54.887827 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpv41tN1/file156cd1ab8b775/features/data_transformed.tsv
2025-08-18 22:24:54.890188 INFO::Applying z-score to standardize continuous metadata
2025-08-18 22:24:54.895859 INFO::Running the linear model component
2025-08-18 22:24:54.919089 INFO::Fitting model to feature number 1, a
2025-08-18 22:24:54.924653 INFO::Fitting model to feature number 2, b
2025-08-18 22:24:54.92954 INFO::Fitting model to feature number 3, c
2025-08-18 22:24:54.938672 INFO::Counting total values for each feature
2025-08-18 22:24:54.94134 INFO::Running the logistic model component
2025-08-18 22:24:54.966483 INFO::Fitting model to feature number 1, a
2025-08-18 22:24:54.973475 INFO::Fitting model to feature number 2, b
2025-08-18 22:24:54.993778 INFO::Fitting model to feature number 3, c
2025-08-18 22:24:55.002961 INFO::Counting total values for each feature
2025-08-18 22:24:55.005225 INFO::Re-running abundances for warn_prevalence
2025-08-18 22:24:55.006625 INFO::Running selected normalization method: TSS
2025-08-18 22:24:55.008253 INFO::Running selected transform method: LOG
2025-08-18 22:24:55.026961 INFO::Fitting model to feature number 1, a
2025-08-18 22:24:55.031941 INFO::Fitting model to feature number 2, b
2025-08-18 22:24:55.037931 INFO::Fitting model to feature number 3, c
2025-08-18 22:24:55.13611 INFO::Creating fits folder
2025-08-18 22:24:55.137564 INFO::Writing residuals to file /tmp/Rtmpv41tN1/file156cd1ab8b775/fits/residuals_linear.rds
2025-08-18 22:24:55.139023 INFO::Writing fitted values to file /tmp/Rtmpv41tN1/file156cd1ab8b775/fits/fitted_linear.rds
2025-08-18 22:24:55.140651 INFO::Writing residuals to file /tmp/Rtmpv41tN1/file156cd1ab8b775/fits/residuals_logistic.rds
2025-08-18 22:24:55.14254 INFO::Writing fitted values to file /tmp/Rtmpv41tN1/file156cd1ab8b775/fits/fitted_logistic.rds
2025-08-18 22:24:55.145691 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmpv41tN1/file156cd1ab8b775/all_results.tsv
2025-08-18 22:24:55.148601 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/Rtmpv41tN1/file156cd1ab8b775/significant_results.tsv
2025-08-18 22:24:55.151269 INFO::Creating output figures folder
2025-08-18 22:24:55.153566 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmpv41tN1/file156cd1ab8b775/figures/summary_plot.pdf
2025-08-18 22:24:56.50328 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpv41tN1/file156cd1ab8b775/figures
2025-08-18 22:24:56.506212 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-18 22:24:56.511779 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-18 22:24:56.915863 INFO::Writing summary plot of
                        significant results to file: /tmp/Rtmpv41tN1/file156cd1ab8b775/figures/summary_plot.pdf
2025-08-18 22:24:58.402669 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpv41tN1/file156cd1ab8b775/figures
2025-08-18 22:24:58.404966 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-18 22:24:58.411631 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-18 22:24:58.851112 INFO::Running the linear model component
2025-08-18 22:24:58.865342 INFO::Fitting model to feature number 1, a
2025-08-18 22:24:58.87264 INFO::Fitting model to feature number 2, b
2025-08-18 22:24:58.879208 INFO::Fitting model to feature number 3, c
2025-08-18 22:24:58.887456 INFO::Counting total values for each feature
2025-08-18 22:24:58.889109 INFO::Running the logistic model component
2025-08-18 22:24:58.901043 INFO::Fitting model to feature number 1, a
2025-08-18 22:24:58.908396 INFO::Fitting model to feature number 2, b
2025-08-18 22:24:58.91388 INFO::Fitting model to feature number 3, c
2025-08-18 22:24:58.922117 INFO::Counting total values for each feature
2025-08-18 22:24:58.92515 INFO::Re-running abundances for warn_prevalence
2025-08-18 22:24:58.92646 INFO::Running selected normalization method: TSS
2025-08-18 22:24:58.928631 INFO::Running selected transform method: LOG
2025-08-18 22:24:58.940696 INFO::Fitting model to feature number 1, a
2025-08-18 22:24:58.945691 INFO::Fitting model to feature number 2, b
2025-08-18 22:24:58.95046 INFO::Fitting model to feature number 3, c
2025-08-18 22:24:59.066758 INFO::Creating output folder
2025-08-18 22:24:59.06787 INFO::Creating output figures folder
2025-08-18 22:24:59.069211 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmpv41tN1/file156cd5aa9fff0/figures/summary_plot.pdf
2025-08-18 22:25:00.527019 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpv41tN1/file156cd5aa9fff0/figures
2025-08-18 22:25:00.529304 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-18 22:25:00.536335 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-18 22:25:01.633173 INFO::Applying z-score to standardize continuous metadata
2025-08-18 22:25:01.641877 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-18 22:25:01.642739 INFO::Bypass z-score application to metadata
2025-08-18 22:25:01.645215 INFO::Bypass z-score application to metadata
2025-08-18 22:25:01.670003 INFO::Determining format of input files
2025-08-18 22:25:01.671523 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-18 22:25:01.672919 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-18 22:25:01.684376 INFO::Determining format of input files
2025-08-18 22:25:01.685508 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-18 22:25:01.68678 INFO::Input format is feature_specific_covariate samples as columns
2025-08-18 22:25:01.69528 INFO::Determining format of input files
2025-08-18 22:25:01.696784 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-18 22:25:01.698275 INFO::Input format is feature_specific_covariate samples as columns
2025-08-18 22:25:01.700723 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-18 22:25:01.701874 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-18 22:25:01.717427 INFO::Running selected transform method: LOG
2025-08-18 22:25:01.719285 INFO::Creating output feature tables folder
2025-08-18 22:25:01.72099 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpv41tN1/file156cd4b20cbde/features/data_transformed.tsv
2025-08-18 22:25:01.727858 INFO::Running selected transform method: LOG
2025-08-18 22:25:01.729054 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpv41tN1/file156cd4b20cbde/features/data_transformed.tsv
2025-08-18 22:25:01.734495 INFO::Running selected transform method: PLOG
2025-08-18 22:25:01.736803 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpv41tN1/file156cd4b20cbde/features/data_transformed.tsv
2025-08-18 22:25:01.740912 INFO::Running selected transform method: NONE
2025-08-18 22:25:01.742125 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpv41tN1/file156cd4b20cbde/features/data_transformed.tsv
2025-08-18 22:25:01.755409 INFO::Running the linear model component
2025-08-18 22:25:01.766784 INFO::Fitting model to feature number 1, a
2025-08-18 22:25:01.772871 INFO::Fitting model to feature number 2, b
2025-08-18 22:25:01.77827 INFO::Fitting model to feature number 3, c
2025-08-18 22:25:01.788695 INFO::Counting total values for each feature
2025-08-18 22:25:01.790788 INFO::Running the logistic model component
2025-08-18 22:25:01.803598 INFO::Fitting model to feature number 1, a
2025-08-18 22:25:01.812153 INFO::Fitting model to feature number 2, b
2025-08-18 22:25:01.817984 INFO::Fitting model to feature number 3, c
2025-08-18 22:25:01.829795 INFO::Counting total values for each feature
2025-08-18 22:25:01.83206 INFO::Re-running abundances for warn_prevalence
2025-08-18 22:25:01.833324 INFO::Running selected normalization method: TSS
2025-08-18 22:25:01.835377 INFO::Running selected transform method: LOG
2025-08-18 22:25:01.847452 INFO::Fitting model to feature number 1, a
2025-08-18 22:25:01.853432 INFO::Fitting model to feature number 2, b
2025-08-18 22:25:01.859692 INFO::Fitting model to feature number 3, c
2025-08-18 22:25:02.000268 INFO::Creating output folder
2025-08-18 22:25:02.001464 INFO::Creating fits folder
2025-08-18 22:25:02.002454 INFO::Writing residuals to file /tmp/Rtmpv41tN1/file156cd5628825a/fits/residuals_linear.rds
2025-08-18 22:25:02.003821 INFO::Writing fitted values to file /tmp/Rtmpv41tN1/file156cd5628825a/fits/fitted_linear.rds
2025-08-18 22:25:02.005534 INFO::Writing residuals to file /tmp/Rtmpv41tN1/file156cd5628825a/fits/residuals_logistic.rds
2025-08-18 22:25:02.007181 INFO::Writing fitted values to file /tmp/Rtmpv41tN1/file156cd5628825a/fits/fitted_logistic.rds
2025-08-18 22:25:02.011139 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmpv41tN1/file156cd5628825a/all_results.tsv
2025-08-18 22:25:02.013608 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/Rtmpv41tN1/file156cd5628825a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
348.324   7.502 357.905

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin323.715 1.03625.007
maaslin_check_arguments0.1560.0040.163
maaslin_check_formula0.1730.0100.184
maaslin_compute_formula0.1630.0100.174
maaslin_contrast_test19.553 0.97820.725
maaslin_filter1.4180.2631.706
maaslin_fit14.752 0.78415.646
maaslin_log_arguments0.1640.0090.174
maaslin_normalize0.3370.0210.361
maaslin_plot_results41.171 1.01742.489
maaslin_plot_results_from_output42.451 1.16443.906
maaslin_process_metadata0.6500.0430.699
maaslin_read_data0.1700.0110.184
maaslin_reorder_data0.1660.0120.181
maaslin_transform0.8110.0670.887
maaslin_write_results16.559 0.68517.381
maaslin_write_results_lefse_format18.060 0.67518.828
preprocess_dna_mtx0.0030.0010.004
preprocess_taxa_mtx0.0040.0010.004