Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-28 12:04 -0400 (Tue, 28 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
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: 2025-10-27 13:45 -0400 (Mon, 27 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

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: 2025-10-27 22:40:20 -0400 (Mon, 27 Oct 2025)
EndedAt: 2025-10-27 22:53:56 -0400 (Mon, 27 Oct 2025)
EllapsedTime: 816.0 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   50.952  1.182  52.510
maaslin_plot_results               50.647  1.441  52.470
maaslin3                           23.656  1.053  24.939
maaslin_contrast_test              20.890  1.082  22.121
maaslin_write_results_lefse_format 16.715  0.706  17.488
maaslin_write_results              16.356  0.806  17.258
maaslin_fit                        14.324  0.817  15.229
* 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")
2025-10-27 22:47:31.158102 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:47:31.93625 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:47:32.044169 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:47:32.073427 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:47:32.121415 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:47:32.23243 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:47:32.240916 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:47:32.257347 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:47:32.368913 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:47:32.376242 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:47:32.445211 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:47:32.501164 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:47:32.53172 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:47:32.583854 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:47:32.678306 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:47:50.635212 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:47:50.723905 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:47:50.823115 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:47:50.851384 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:47:50.901917 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:47:50.993173 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:47:51.00317 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:47:51.021307 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:47:51.183102 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:47:51.190126 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:47:51.260207 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:47:51.315384 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:47:51.329856 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:47:51.382998 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:47:51.463751 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:47:56.093 R[66258:654294583] XType: com.apple.fonts is not accessible.
2025-10-27 22:47:56.093 R[66258:654294583] XType: XTFontStaticRegistry is enabled.
2025-10-27 22:48:18.957693 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:48:19.066527 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:48:19.162911 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:48:19.191067 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:48:19.23313 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:48:19.330145 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:48:19.338425 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:48:19.355659 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:48:20.384797 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:48:20.391773 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:48:20.454614 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:48:20.505871 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:48:20.521869 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:48:20.575036 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:48:20.667985 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:48:35.90264 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:48:35.999611 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:48:36.099178 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:48:36.126254 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:48:36.176959 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:48:36.277705 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:48:36.285759 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:48:36.303158 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:48:36.429051 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:48:36.437511 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:48:36.504502 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:48:36.556528 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:48:36.573111 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:48:36.627744 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:48:36.719568 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:48:36.979262 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/residuals_linear.rds
2025-10-27 22:48:37.044141 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/fitted_linear.rds
2025-10-27 22:48:37.112799 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/residuals_logistic.rds
2025-10-27 22:48:37.481748 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/fitted_logistic.rds
2025-10-27 22:49:02.651935 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:49:02.766353 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:49:02.874398 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:49:02.907602 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:49:02.958078 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:49:03.060901 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:49:03.067854 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:49:03.0826 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:49:03.213568 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:49:03.222054 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:49:03.285653 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:49:03.336238 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:49:03.350492 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:49:03.4069 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:49:03.502721 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:49:18.68352 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:49:18.776325 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:49:18.86197 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:49:18.891758 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:49:18.930165 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:49:19.014717 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:49:19.021772 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:49:19.034825 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:49:19.146786 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:49:19.153493 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:49:19.211177 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:49:19.260248 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:49:19.276028 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:49:19.322474 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:49:19.40808 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:49:19.666449 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/residuals_linear.rds
2025-10-27 22:49:19.737659 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/fitted_linear.rds
2025-10-27 22:49:19.812079 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/residuals_logistic.rds
2025-10-27 22:49:20.152306 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/fitted_logistic.rds
2025-10-27 22:49:44.467849 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:49:44.573718 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:49:44.677881 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:49:44.712088 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:49:44.761399 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:49:44.868903 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:49:44.877238 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:49:44.895515 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:49:45.027716 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:49:45.036563 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:49:45.112446 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:49:45.16772 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:49:45.184835 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:49:45.243605 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:49:45.343183 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:50:00.492878 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:50:00.587518 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:50:00.691873 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:50:00.721508 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:50:00.762982 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:50:00.866853 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:50:00.875018 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:50:00.891718 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:50:01.026427 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:50:01.034148 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:50:01.100358 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:50:01.16174 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:50:01.177374 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:50:01.230335 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:50:01.322427 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:50:01.630332 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/residuals_linear.rds
2025-10-27 22:50:01.696435 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/fitted_linear.rds
2025-10-27 22:50:01.759673 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/residuals_logistic.rds
2025-10-27 22:50:02.112338 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d26a1f7038/fits/fitted_logistic.rds
2025-10-27 22:50:26.422793 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:50:26.51363 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:50:26.605329 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:50:26.634715 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:50:26.681112 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:50:26.775114 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:50:26.783265 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:50:26.800089 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:50:26.925873 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:50:26.93407 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:50:26.998473 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:50:27.05424 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:50:27.073964 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:50:27.126666 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:50:27.215258 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:50:41.120023 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:50:41.213581 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:50:41.307013 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:50:41.333941 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:50:41.379209 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:50:41.524069 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:50:41.532924 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:50:41.55078 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:50:41.669638 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:50:41.675619 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:50:41.734964 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:50:41.781938 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:50:41.797123 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:50:41.845763 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:50:41.926015 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:51:08.444139 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:51:19.329527 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:51:45.65889 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:51:56.349282 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:51:56.902949 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_linear.rds
2025-10-27 22:51:56.961596 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_linear.rds
2025-10-27 22:51:57.002385 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_logistic.rds
2025-10-27 22:51:57.094157 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_logistic.rds
2025-10-27 22:52:16.9811 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:52:23.102623 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:52:23.406209 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_linear.rds
2025-10-27 22:52:23.46827 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_linear.rds
2025-10-27 22:52:23.502304 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_logistic.rds
2025-10-27 22:52:23.566198 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_logistic.rds
2025-10-27 22:52:41.200885 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:52:47.62518 WARNING::Fitting problem for feature 124 returning NA
2025-10-27 22:52:47.939155 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_linear.rds
2025-10-27 22:52:48.00987 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_linear.rds
2025-10-27 22:52:48.047466 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_logistic.rds
2025-10-27 22:52:48.113034 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_logistic.rds
2025-10-27 22:53:04.576779 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:53:04.646204 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:53:04.713947 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:53:04.733905 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:53:04.766036 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:53:04.836277 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:53:04.841635 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:53:04.852998 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:53:04.979286 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:53:04.984424 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:53:05.029444 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:53:05.065796 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:53:05.07731 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:53:05.117407 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:53:05.179494 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:53:16.241794 WARNING::Fitting problem for feature 50 returning NA
2025-10-27 22:53:16.318272 WARNING::Fitting problem for feature 62 returning NA
2025-10-27 22:53:16.388077 WARNING::Fitting problem for feature 74 returning NA
2025-10-27 22:53:16.408178 WARNING::Fitting problem for feature 78 returning NA
2025-10-27 22:53:16.442129 WARNING::Fitting problem for feature 84 returning NA
2025-10-27 22:53:16.512499 WARNING::Fitting problem for feature 96 returning NA
2025-10-27 22:53:16.517972 WARNING::Fitting problem for feature 97 returning NA
2025-10-27 22:53:16.529862 WARNING::Fitting problem for feature 99 returning NA
2025-10-27 22:53:16.618343 WARNING::Fitting problem for feature 114 returning NA
2025-10-27 22:53:16.623382 WARNING::Fitting problem for feature 115 returning NA
2025-10-27 22:53:16.668424 WARNING::Fitting problem for feature 123 returning NA
2025-10-27 22:53:16.775768 WARNING::Fitting problem for feature 130 returning NA
2025-10-27 22:53:16.787284 WARNING::Fitting problem for feature 132 returning NA
2025-10-27 22:53:16.825061 WARNING::Fitting problem for feature 139 returning NA
2025-10-27 22:53:16.886863 WARNING::Fitting problem for feature 150 returning NA
2025-10-27 22:53:17.104523 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_linear.rds
2025-10-27 22:53:17.165911 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_linear.rds
2025-10-27 22:53:17.2293 WARNING::Deleting existing residuals file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/residuals_logistic.rds
2025-10-27 22:53:17.523535 WARNING::Deleting existing fitted file: /tmp/RtmpTohPU0/file102d2dbd42b/fits/fitted_logistic.rds
2025-10-27 22:53:35.78641 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-27 22:53:35.803979 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-27 22:53:35.814871 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-27 22:53:35.866675 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-27 22:53:35.883482 ERROR::Effect name not found in metadata: d
2025-10-27 22:53:35.895526 ERROR::No user formula provided
2025-10-27 22:53:35.931168 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-27 22:53:35.94764 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-27 22:53:39.019185 INFO::Writing function arguments to log file
2025-10-27 22:53:39.040164 INFO::Verifying options selected are valid
2025-10-27 22:53:41.320546 INFO::Writing function arguments to log file
2025-10-27 22:53:41.338028 INFO::Verifying options selected are valid
2025-10-27 22:53:41.339267 INFO::Determining format of input files
2025-10-27 22:53:41.34028 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-27 22:53:41.342949 INFO::Running selected normalization method: TSS
2025-10-27 22:53:41.344397 INFO::Creating output feature tables folder
2025-10-27 22:53:41.345764 INFO::Writing normalized data to file /tmp/RtmpTohPU0/file102d26ce2c073/features/data_norm.tsv
2025-10-27 22:53:41.347445 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-27 22:53:41.348367 INFO::Total samples in data: 16
2025-10-27 22:53:41.349381 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-27 22:53:41.350276 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-27 22:53:41.352606 INFO::Total filtered features: 0
2025-10-27 22:53:41.354151 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-27 22:53:41.355988 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-27 22:53:41.357466 INFO::Filtered feature names from variance filtering:
2025-10-27 22:53:41.358859 INFO::Writing filtered data to file /tmp/RtmpTohPU0/file102d26ce2c073/features/filtered_data.tsv
2025-10-27 22:53:41.361375 INFO::Running selected transform method: LOG
2025-10-27 22:53:41.362704 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTohPU0/file102d26ce2c073/features/data_transformed.tsv
2025-10-27 22:53:41.364756 INFO::Applying z-score to standardize continuous metadata
2025-10-27 22:53:41.370486 INFO::Running the linear model component
2025-10-27 22:53:41.389858 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:41.394725 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:41.39896 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:41.405977 INFO::Counting total values for each feature
2025-10-27 22:53:41.407888 INFO::Running the logistic model component
2025-10-27 22:53:41.429288 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:41.435914 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:41.444679 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:41.454818 INFO::Counting total values for each feature
2025-10-27 22:53:41.457167 INFO::Re-running abundances for warn_prevalence
2025-10-27 22:53:41.458327 INFO::Running selected normalization method: TSS
2025-10-27 22:53:41.460284 INFO::Running selected transform method: LOG
2025-10-27 22:53:41.479753 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:41.485207 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:41.490596 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:41.581663 INFO::Creating fits folder
2025-10-27 22:53:41.583576 INFO::Writing residuals to file /tmp/RtmpTohPU0/file102d26ce2c073/fits/residuals_linear.rds
2025-10-27 22:53:41.585148 INFO::Writing fitted values to file /tmp/RtmpTohPU0/file102d26ce2c073/fits/fitted_linear.rds
2025-10-27 22:53:41.586586 INFO::Writing residuals to file /tmp/RtmpTohPU0/file102d26ce2c073/fits/residuals_logistic.rds
2025-10-27 22:53:41.58832 INFO::Writing fitted values to file /tmp/RtmpTohPU0/file102d26ce2c073/fits/fitted_logistic.rds
2025-10-27 22:53:41.591026 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpTohPU0/file102d26ce2c073/all_results.tsv
2025-10-27 22:53:41.592933 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/RtmpTohPU0/file102d26ce2c073/significant_results.tsv
2025-10-27 22:53:41.594511 INFO::Creating output figures folder
2025-10-27 22:53:41.595993 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpTohPU0/file102d26ce2c073/figures/summary_plot.pdf
2025-10-27 22:53:43.123393 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTohPU0/file102d26ce2c073/figures
2025-10-27 22:53:43.125343 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-27 22:53:43.130477 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-27 22:53:43.586602 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpTohPU0/file102d26ce2c073/figures/summary_plot.pdf
2025-10-27 22:53:45.094177 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTohPU0/file102d26ce2c073/figures
2025-10-27 22:53:45.095657 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-27 22:53:45.100564 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-27 22:53:45.564144 INFO::Running the linear model component
2025-10-27 22:53:45.571659 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:45.575718 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:45.579249 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:45.585272 INFO::Counting total values for each feature
2025-10-27 22:53:45.586716 INFO::Running the logistic model component
2025-10-27 22:53:45.594084 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:45.599981 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:45.605288 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:45.613116 INFO::Counting total values for each feature
2025-10-27 22:53:45.614928 INFO::Re-running abundances for warn_prevalence
2025-10-27 22:53:45.615649 INFO::Running selected normalization method: TSS
2025-10-27 22:53:45.616838 INFO::Running selected transform method: LOG
2025-10-27 22:53:45.623823 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:45.627443 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:45.630845 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:45.705315 INFO::Creating output folder
2025-10-27 22:53:45.706363 INFO::Creating output figures folder
2025-10-27 22:53:45.707591 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpTohPU0/file102d229fdb50a/figures/summary_plot.pdf
2025-10-27 22:53:47.10639 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTohPU0/file102d229fdb50a/figures
2025-10-27 22:53:47.107791 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-27 22:53:47.112126 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-27 22:53:48.065726 INFO::Applying z-score to standardize continuous metadata
2025-10-27 22:53:48.072956 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-27 22:53:48.073759 INFO::Bypass z-score application to metadata
2025-10-27 22:53:48.076579 INFO::Bypass z-score application to metadata
2025-10-27 22:53:48.095906 INFO::Determining format of input files
2025-10-27 22:53:48.096802 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-27 22:53:48.097537 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-27 22:53:48.104803 INFO::Determining format of input files
2025-10-27 22:53:48.105947 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-27 22:53:48.107241 INFO::Input format is feature_specific_covariate samples as columns
2025-10-27 22:53:48.114339 INFO::Determining format of input files
2025-10-27 22:53:48.11526 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-27 22:53:48.116204 INFO::Input format is feature_specific_covariate samples as columns
2025-10-27 22:53:48.117867 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-27 22:53:48.118608 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-27 22:53:48.13049 INFO::Running selected transform method: LOG
2025-10-27 22:53:48.131737 INFO::Creating output feature tables folder
2025-10-27 22:53:48.132766 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTohPU0/file102d25791b6ae/features/data_transformed.tsv
2025-10-27 22:53:48.137011 INFO::Running selected transform method: LOG
2025-10-27 22:53:48.138093 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTohPU0/file102d25791b6ae/features/data_transformed.tsv
2025-10-27 22:53:48.141743 INFO::Running selected transform method: PLOG
2025-10-27 22:53:48.143134 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTohPU0/file102d25791b6ae/features/data_transformed.tsv
2025-10-27 22:53:48.146185 INFO::Running selected transform method: NONE
2025-10-27 22:53:48.146856 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTohPU0/file102d25791b6ae/features/data_transformed.tsv
2025-10-27 22:53:48.156031 INFO::Running the linear model component
2025-10-27 22:53:48.164005 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:48.16791 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:48.171589 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:48.177874 INFO::Counting total values for each feature
2025-10-27 22:53:48.179344 INFO::Running the logistic model component
2025-10-27 22:53:48.186641 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:48.192118 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:48.197708 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:48.205603 INFO::Counting total values for each feature
2025-10-27 22:53:48.207371 INFO::Re-running abundances for warn_prevalence
2025-10-27 22:53:48.208065 INFO::Running selected normalization method: TSS
2025-10-27 22:53:48.209226 INFO::Running selected transform method: LOG
2025-10-27 22:53:48.217845 INFO::Fitting model to feature number 1, a
2025-10-27 22:53:48.221522 INFO::Fitting model to feature number 2, b
2025-10-27 22:53:48.224958 INFO::Fitting model to feature number 3, c
2025-10-27 22:53:48.303491 INFO::Creating output folder
2025-10-27 22:53:48.304504 INFO::Creating fits folder
2025-10-27 22:53:48.305391 INFO::Writing residuals to file /tmp/RtmpTohPU0/file102d21f70866c/fits/residuals_linear.rds
2025-10-27 22:53:48.306517 INFO::Writing fitted values to file /tmp/RtmpTohPU0/file102d21f70866c/fits/fitted_linear.rds
2025-10-27 22:53:48.307556 INFO::Writing residuals to file /tmp/RtmpTohPU0/file102d21f70866c/fits/residuals_logistic.rds
2025-10-27 22:53:48.308582 INFO::Writing fitted values to file /tmp/RtmpTohPU0/file102d21f70866c/fits/fitted_logistic.rds
2025-10-27 22:53:48.310889 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpTohPU0/file102d21f70866c/all_results.tsv
2025-10-27 22:53:48.31307 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/RtmpTohPU0/file102d21f70866c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
379.512   7.955 389.631

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin323.656 1.05324.939
maaslin_check_arguments0.1730.0050.181
maaslin_check_formula0.1660.0100.177
maaslin_compute_formula0.1660.0100.177
maaslin_contrast_test20.890 1.08222.121
maaslin_filter0.6250.0490.679
maaslin_fit14.324 0.81715.229
maaslin_log_arguments0.1600.0090.171
maaslin_normalize0.3680.0250.397
maaslin_plot_results50.647 1.44152.470
maaslin_plot_results_from_output50.952 1.18252.510
maaslin_process_metadata0.6230.0400.668
maaslin_read_data0.1790.0100.189
maaslin_reorder_data0.1760.0100.187
maaslin_transform0.7760.0500.832
maaslin_write_results16.356 0.80617.258
maaslin_write_results_lefse_format16.715 0.70617.488
preprocess_dna_mtx0.0040.0010.005
preprocess_taxa_mtx0.0060.0010.006