Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-20 12:06 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1164/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 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    OK    OK  

CHECK results for maaslin3 on kjohnson3

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: 2025-10-19 20:25:40 -0400 (Sun, 19 Oct 2025)
EndedAt: 2025-10-19 20:30:31 -0400 (Sun, 19 Oct 2025)
EllapsedTime: 290.7 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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   16.293  0.777  17.754
maaslin_plot_results               16.206  0.813  18.445
maaslin3                            8.300  0.508   9.184
maaslin_contrast_test               7.103  0.547   7.771
maaslin_write_results               6.136  0.571   6.744
maaslin_write_results_lefse_format  6.016  0.537   6.590
maaslin_fit                         4.955  0.606   5.823
* 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-arm64/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: aarch64-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")
2025-10-19 20:28:10.145458 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:10.172213 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:10.205744 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:10.213066 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:10.224266 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:10.248675 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:10.250541 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:10.254341 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:10.28867 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:10.290582 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:10.306263 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:10.319129 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:10.323134 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:10.339407 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:10.361419 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:28:17.120231 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:17.146083 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:17.171441 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:17.178939 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:17.190632 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:17.216711 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:17.218717 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:17.222798 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:17.264465 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:17.266466 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:17.283516 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:17.297215 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:17.301379 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:17.315334 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:17.339233 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:28:18.790 R[48238:498595345] XType: Using static font registry.
2025-10-19 20:28:26.634497 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:26.659202 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:26.684389 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:26.692004 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:26.704047 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:26.732562 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:26.734769 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:26.738907 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:26.771921 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:26.773969 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:26.791281 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:26.806112 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:26.810626 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:26.825185 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:26.850033 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:28:31.984627 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:32.010289 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:32.045534 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:32.052928 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:32.064345 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:32.089192 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:32.091135 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:32.095487 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:32.128928 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:32.131106 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:32.149311 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:32.16359 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:32.167739 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:32.181924 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:32.206322 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:28:32.277949 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_linear.rds
2025-10-19 20:28:32.310544 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_linear.rds
2025-10-19 20:28:32.34441 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_logistic.rds
2025-10-19 20:28:32.510548 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_logistic.rds
2025-10-19 20:28:40.333606 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:40.359635 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:40.385204 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:40.392852 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:40.40494 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:40.431679 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:40.433719 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:40.437796 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:40.46785 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:40.469716 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:40.485564 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:40.498343 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:40.569524 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:40.58317 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:40.604918 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:28:45.690153 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:45.717612 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:45.74529 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:45.753398 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:45.766043 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:45.818367 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:45.820422 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:45.824441 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:45.857762 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:45.859718 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:45.87627 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:45.889779 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:45.893888 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:45.907289 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:45.929889 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:28:46.002354 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_linear.rds
2025-10-19 20:28:46.035804 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_linear.rds
2025-10-19 20:28:46.069462 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_logistic.rds
2025-10-19 20:28:46.236673 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_logistic.rds
2025-10-19 20:28:54.390439 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:28:54.417466 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:28:54.444051 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:28:54.452052 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:28:54.464213 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:28:54.507886 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:28:54.511215 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:28:54.516119 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:28:54.550978 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:28:54.553388 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:28:54.571743 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:28:54.586075 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:28:54.590495 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:28:54.604802 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:28:54.629686 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:29:00.063203 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:29:00.088917 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:29:00.114271 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:29:00.121795 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:29:00.133452 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:29:00.159239 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:29:00.161191 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:29:00.165229 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:29:00.197722 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:29:00.199682 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:29:00.216521 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:29:00.229905 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:29:00.234125 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:29:00.247812 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:29:00.270972 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:29:00.365403 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_linear.rds
2025-10-19 20:29:00.397602 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_linear.rds
2025-10-19 20:29:00.431389 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/residuals_logistic.rds
2025-10-19 20:29:00.601355 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e31b6de8/fits/fitted_logistic.rds
2025-10-19 20:29:08.606385 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:29:08.637378 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:29:08.665502 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:29:08.673735 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:29:08.686323 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:29:08.713349 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:29:08.715408 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:29:08.71962 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:29:08.754272 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:29:08.756332 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:29:08.773899 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:29:08.788812 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:29:08.793061 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:29:08.807086 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:29:08.831081 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:29:13.472059 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:29:13.498957 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:29:13.524542 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:29:13.532455 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:29:13.543917 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:29:13.568901 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:29:13.570829 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:29:13.574747 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:29:13.606435 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:29:13.608407 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:29:13.624997 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:29:13.638465 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:29:13.642687 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:29:13.656341 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:29:13.679625 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:29:23.269318 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:29:26.628746 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:29:36.051319 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:29:40.051183 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:29:40.248168 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds
2025-10-19 20:29:40.280598 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds
2025-10-19 20:29:40.303281 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds
2025-10-19 20:29:40.344751 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds
2025-10-19 20:29:49.067252 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:29:51.282919 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:29:51.407707 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds
2025-10-19 20:29:51.441488 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds
2025-10-19 20:29:51.464261 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds
2025-10-19 20:29:51.505187 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds
2025-10-19 20:29:58.892382 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:30:01.622293 WARNING::Fitting problem for feature 124 returning NA
2025-10-19 20:30:01.729515 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds
2025-10-19 20:30:01.762835 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds
2025-10-19 20:30:01.786022 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds
2025-10-19 20:30:01.826617 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds
2025-10-19 20:30:08.995731 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:30:09.023128 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:30:09.049885 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:30:09.057871 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:30:09.070547 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:30:09.097466 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:30:09.099569 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:30:09.103624 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:30:09.13601 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:30:09.138017 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:30:09.155173 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:30:09.1691 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:30:09.173558 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:30:09.187609 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:30:09.235572 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:30:14.268416 WARNING::Fitting problem for feature 50 returning NA
2025-10-19 20:30:14.293872 WARNING::Fitting problem for feature 62 returning NA
2025-10-19 20:30:14.319636 WARNING::Fitting problem for feature 74 returning NA
2025-10-19 20:30:14.327334 WARNING::Fitting problem for feature 78 returning NA
2025-10-19 20:30:14.339066 WARNING::Fitting problem for feature 84 returning NA
2025-10-19 20:30:14.365076 WARNING::Fitting problem for feature 96 returning NA
2025-10-19 20:30:14.367128 WARNING::Fitting problem for feature 97 returning NA
2025-10-19 20:30:14.371284 WARNING::Fitting problem for feature 99 returning NA
2025-10-19 20:30:14.404004 WARNING::Fitting problem for feature 114 returning NA
2025-10-19 20:30:14.406032 WARNING::Fitting problem for feature 115 returning NA
2025-10-19 20:30:14.422883 WARNING::Fitting problem for feature 123 returning NA
2025-10-19 20:30:14.436757 WARNING::Fitting problem for feature 130 returning NA
2025-10-19 20:30:14.440983 WARNING::Fitting problem for feature 132 returning NA
2025-10-19 20:30:14.454899 WARNING::Fitting problem for feature 139 returning NA
2025-10-19 20:30:14.478387 WARNING::Fitting problem for feature 150 returning NA
2025-10-19 20:30:14.564572 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_linear.rds
2025-10-19 20:30:14.597172 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_linear.rds
2025-10-19 20:30:14.631013 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/residuals_logistic.rds
2025-10-19 20:30:14.796699 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e6bc8d770/fits/fitted_logistic.rds
2025-10-19 20:30:22.486367 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-19 20:30:22.492163 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-19 20:30:22.49605 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-19 20:30:22.513357 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-19 20:30:22.519205 ERROR::Effect name not found in metadata: d
2025-10-19 20:30:22.523204 ERROR::No user formula provided
2025-10-19 20:30:22.534412 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-19 20:30:22.538736 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-19 20:30:23.555448 INFO::Writing function arguments to log file
2025-10-19 20:30:23.561087 INFO::Verifying options selected are valid
2025-10-19 20:30:24.399571 INFO::Writing function arguments to log file
2025-10-19 20:30:24.404093 INFO::Verifying options selected are valid
2025-10-19 20:30:24.404464 INFO::Determining format of input files
2025-10-19 20:30:24.404786 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-19 20:30:24.405568 INFO::Running selected normalization method: TSS
2025-10-19 20:30:24.406066 INFO::Creating output feature tables folder
2025-10-19 20:30:24.406462 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/features/data_norm.tsv
2025-10-19 20:30:24.407084 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-19 20:30:24.407409 INFO::Total samples in data: 16
2025-10-19 20:30:24.407689 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-19 20:30:24.407962 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-19 20:30:24.408577 INFO::Total filtered features: 0
2025-10-19 20:30:24.408909 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-19 20:30:24.409282 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-19 20:30:24.409582 INFO::Filtered feature names from variance filtering:
2025-10-19 20:30:24.409857 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/features/filtered_data.tsv
2025-10-19 20:30:24.410404 INFO::Running selected transform method: LOG
2025-10-19 20:30:24.410791 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/features/data_transformed.tsv
2025-10-19 20:30:24.411376 INFO::Applying z-score to standardize continuous metadata
2025-10-19 20:30:24.413177 INFO::Running the linear model component
2025-10-19 20:30:24.418215 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:24.4197 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:24.42101 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:24.423288 INFO::Counting total values for each feature
2025-10-19 20:30:24.423941 INFO::Running the logistic model component
2025-10-19 20:30:24.429122 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:24.431253 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:24.433163 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:24.435979 INFO::Counting total values for each feature
2025-10-19 20:30:24.436748 INFO::Re-running abundances for warn_prevalence
2025-10-19 20:30:24.437129 INFO::Running selected normalization method: TSS
2025-10-19 20:30:24.437639 INFO::Running selected transform method: LOG
2025-10-19 20:30:24.442772 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:24.444178 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:24.445474 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:24.470894 INFO::Creating fits folder
2025-10-19 20:30:24.471444 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/residuals_linear.rds
2025-10-19 20:30:24.471943 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/fitted_linear.rds
2025-10-19 20:30:24.472408 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/residuals_logistic.rds
2025-10-19 20:30:24.472861 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/fits/fitted_logistic.rds
2025-10-19 20:30:24.473756 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/all_results.tsv
2025-10-19 20:30:24.474401 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/significant_results.tsv
2025-10-19 20:30:24.474905 INFO::Creating output figures folder
2025-10-19 20:30:24.47539 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures/summary_plot.pdf
2025-10-19 20:30:25.05034 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures
2025-10-19 20:30:25.051118 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-19 20:30:25.053121 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-19 20:30:25.252552 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures/summary_plot.pdf
2025-10-19 20:30:25.832559 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e7da5aa24/figures
2025-10-19 20:30:25.83314 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-19 20:30:25.834931 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-19 20:30:26.026475 INFO::Running the linear model component
2025-10-19 20:30:26.029145 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:26.036124 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:26.037467 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:26.039844 INFO::Counting total values for each feature
2025-10-19 20:30:26.040382 INFO::Running the logistic model component
2025-10-19 20:30:26.042904 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:26.044759 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:26.046504 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:26.049398 INFO::Counting total values for each feature
2025-10-19 20:30:26.050082 INFO::Re-running abundances for warn_prevalence
2025-10-19 20:30:26.050338 INFO::Running selected normalization method: TSS
2025-10-19 20:30:26.050794 INFO::Running selected transform method: LOG
2025-10-19 20:30:26.053513 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:26.054971 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:26.056204 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:26.085517 INFO::Creating output folder
2025-10-19 20:30:26.086043 INFO::Creating output figures folder
2025-10-19 20:30:26.086545 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e4e69f4a4/figures/summary_plot.pdf
2025-10-19 20:30:26.680546 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e4e69f4a4/figures
2025-10-19 20:30:26.681329 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-19 20:30:26.683946 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-19 20:30:27.079483 INFO::Applying z-score to standardize continuous metadata
2025-10-19 20:30:27.082035 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-19 20:30:27.0823 INFO::Bypass z-score application to metadata
2025-10-19 20:30:27.083019 INFO::Bypass z-score application to metadata
2025-10-19 20:30:27.08916 INFO::Determining format of input files
2025-10-19 20:30:27.089436 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-19 20:30:27.089675 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-19 20:30:27.09172 INFO::Determining format of input files
2025-10-19 20:30:27.092029 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-19 20:30:27.092404 INFO::Input format is feature_specific_covariate samples as columns
2025-10-19 20:30:27.094699 INFO::Determining format of input files
2025-10-19 20:30:27.094976 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-19 20:30:27.095276 INFO::Input format is feature_specific_covariate samples as columns
2025-10-19 20:30:27.095733 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-19 20:30:27.095949 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-19 20:30:27.099266 INFO::Running selected transform method: LOG
2025-10-19 20:30:27.09959 INFO::Creating output feature tables folder
2025-10-19 20:30:27.099952 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv
2025-10-19 20:30:27.101211 INFO::Running selected transform method: LOG
2025-10-19 20:30:27.101526 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv
2025-10-19 20:30:27.102655 INFO::Running selected transform method: PLOG
2025-10-19 20:30:27.103131 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv
2025-10-19 20:30:27.104014 INFO::Running selected transform method: NONE
2025-10-19 20:30:27.104246 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e44aa8bde/features/data_transformed.tsv
2025-10-19 20:30:27.106764 INFO::Running the linear model component
2025-10-19 20:30:27.109373 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:27.110743 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:27.111921 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:27.114138 INFO::Counting total values for each feature
2025-10-19 20:30:27.114665 INFO::Running the logistic model component
2025-10-19 20:30:27.11717 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:27.119047 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:27.120838 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:27.123547 INFO::Counting total values for each feature
2025-10-19 20:30:27.124195 INFO::Re-running abundances for warn_prevalence
2025-10-19 20:30:27.124423 INFO::Running selected normalization method: TSS
2025-10-19 20:30:27.124836 INFO::Running selected transform method: LOG
2025-10-19 20:30:27.127441 INFO::Fitting model to feature number 1, a
2025-10-19 20:30:27.12875 INFO::Fitting model to feature number 2, b
2025-10-19 20:30:27.13637 INFO::Fitting model to feature number 3, c
2025-10-19 20:30:27.164742 INFO::Creating output folder
2025-10-19 20:30:27.165181 INFO::Creating fits folder
2025-10-19 20:30:27.165494 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/residuals_linear.rds
2025-10-19 20:30:27.167853 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/fitted_linear.rds
2025-10-19 20:30:27.169269 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/residuals_logistic.rds
2025-10-19 20:30:27.170262 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/fits/fitted_logistic.rds
2025-10-19 20:30:27.171809 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/all_results.tsv
2025-10-19 20:30:27.172442 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpOSIB15/filebc6e18c4bf0a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
135.590   5.469 141.589

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.3000.5089.184
maaslin_check_arguments0.0620.0020.068
maaslin_check_formula0.0560.0040.069
maaslin_compute_formula0.0570.0040.073
maaslin_contrast_test7.1030.5477.771
maaslin_filter0.2090.0180.228
maaslin_fit4.9550.6065.823
maaslin_log_arguments0.0550.0030.072
maaslin_normalize0.1270.0170.201
maaslin_plot_results16.206 0.81318.445
maaslin_plot_results_from_output16.293 0.77717.754
maaslin_process_metadata0.2440.0190.264
maaslin_read_data0.0590.0030.063
maaslin_reorder_data0.0560.0030.060
maaslin_transform0.2730.0280.302
maaslin_write_results6.1360.5716.744
maaslin_write_results_lefse_format6.0160.5376.590
preprocess_dna_mtx0.0010.0000.001
preprocess_taxa_mtx0.0010.0000.001