Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-25 12:06 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1170/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.2  (landing page)
William Nickols
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: e7106d5
git_last_commit_date: 2025-10-12 11:00:51 -0400 (Sun, 12 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    NA    NA  

CHECK results for maaslin3 on 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: 2025-10-24 20:29:09 -0400 (Fri, 24 Oct 2025)
EndedAt: 2025-10-24 20:33:57 -0400 (Fri, 24 Oct 2025)
EllapsedTime: 288.6 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   16.308  0.721  17.089
maaslin_plot_results               16.036  0.698  16.811
maaslin3                            8.023  0.528   8.582
maaslin_contrast_test               7.193  0.644   7.941
maaslin_write_results_lefse_format  5.863  0.527   6.431
maaslin_write_results               5.432  0.537   5.990
maaslin_fit                         4.947  0.645   5.615
* 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")
2025-10-24 20:31:35.884326 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:31:35.911558 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:31:35.945624 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:31:35.95309 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:31:35.965814 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:31:35.992536 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:31:35.994573 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:31:35.998675 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:31:36.035671 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:31:36.037638 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:31:36.054584 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:31:36.068062 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:31:36.072136 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:31:36.089776 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:31:36.112632 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:31:42.534542 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:31:42.561535 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:31:42.587125 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:31:42.594771 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:31:42.606606 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:31:42.632653 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:31:42.634668 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:31:42.638745 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:31:42.673525 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:31:42.675576 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:31:42.702175 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:31:42.715684 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:31:42.719764 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:31:42.732933 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:31:42.755503 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:31:44.209 R[59603:545273272] XType: Using static font registry.
2025-10-24 20:31:52.016758 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:31:52.04465 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:31:52.073466 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:31:52.082457 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:31:52.094812 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:31:52.122441 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:31:52.124594 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:31:52.129277 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:31:52.164345 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:31:52.166558 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:31:52.184254 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:31:52.198572 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:31:52.203004 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:31:52.229894 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:31:52.253881 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:31:57.502716 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:31:57.52956 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:31:57.55613 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:31:57.563728 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:31:57.575539 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:31:57.602156 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:31:57.604174 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:31:57.608285 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:31:57.641372 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:31:57.64352 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:31:57.660544 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:31:57.674896 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:31:57.679234 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:31:57.693544 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:31:57.717461 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:31:57.79822 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/residuals_linear.rds
2025-10-24 20:31:57.830739 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/fitted_linear.rds
2025-10-24 20:31:57.864692 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/residuals_logistic.rds
2025-10-24 20:31:58.036 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/fitted_logistic.rds
2025-10-24 20:32:06.321571 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:32:06.349103 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:32:06.377023 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:32:06.38514 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:32:06.401095 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:32:06.427652 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:32:06.429809 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:32:06.434176 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:32:06.468788 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:32:06.470906 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:32:06.488592 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:32:06.50255 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:32:07.01068 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:32:07.024639 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:32:07.049047 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:32:12.022462 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:32:12.049338 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:32:12.075687 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:32:12.083608 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:32:12.09594 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:32:12.122691 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:32:12.124871 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:32:12.12912 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:32:12.179262 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:32:12.181488 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:32:12.19896 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:32:12.213072 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:32:12.217381 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:32:12.231782 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:32:12.255355 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:32:12.325981 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/residuals_linear.rds
2025-10-24 20:32:12.35824 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/fitted_linear.rds
2025-10-24 20:32:12.392084 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/residuals_logistic.rds
2025-10-24 20:32:12.560608 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/fitted_logistic.rds
2025-10-24 20:32:20.818872 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:32:20.847 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:32:20.873353 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:32:20.881217 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:32:20.89411 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:32:20.928816 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:32:20.931068 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:32:20.935423 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:32:20.988436 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:32:20.990602 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:32:21.009622 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:32:21.024419 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:32:21.028812 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:32:21.043117 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:32:21.068627 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:32:26.162445 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:32:26.188958 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:32:26.218074 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:32:26.225327 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:32:26.236607 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:32:26.263295 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:32:26.265218 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:32:26.269167 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:32:26.302773 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:32:26.304852 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:32:26.322118 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:32:26.336432 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:32:26.341126 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:32:26.356251 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:32:26.382426 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:32:26.470633 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/residuals_linear.rds
2025-10-24 20:32:26.503397 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/fitted_linear.rds
2025-10-24 20:32:26.537363 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/residuals_logistic.rds
2025-10-24 20:32:26.717807 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d347cc65e9/fits/fitted_logistic.rds
2025-10-24 20:32:34.87104 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:32:34.897779 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:32:34.924789 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:32:34.932859 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:32:34.945628 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:32:34.972619 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:32:34.974699 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:32:34.978904 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:32:35.013953 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:32:35.016164 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:32:35.03441 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:32:35.049269 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:32:35.053847 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:32:35.068567 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:32:35.094902 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:32:40.214664 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:32:40.242271 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:32:40.267638 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:32:40.275151 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:32:40.287257 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:32:40.314322 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:32:40.316413 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:32:40.320661 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:32:40.353991 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:32:40.356023 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:32:40.372749 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:32:40.386429 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:32:40.39089 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:32:40.405098 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:32:40.429717 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:32:49.985086 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:32:53.247996 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:02.679575 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:06.600411 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:06.809106 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_linear.rds
2025-10-24 20:33:06.841265 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_linear.rds
2025-10-24 20:33:06.863142 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_logistic.rds
2025-10-24 20:33:06.903217 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_logistic.rds
2025-10-24 20:33:15.668029 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:17.808062 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:17.906203 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_linear.rds
2025-10-24 20:33:17.938969 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_linear.rds
2025-10-24 20:33:17.961829 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_logistic.rds
2025-10-24 20:33:18.002572 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_logistic.rds
2025-10-24 20:33:25.447488 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:28.117369 WARNING::Fitting problem for feature 124 returning NA
2025-10-24 20:33:28.228562 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_linear.rds
2025-10-24 20:33:28.261579 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_linear.rds
2025-10-24 20:33:28.283585 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_logistic.rds
2025-10-24 20:33:28.323684 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_logistic.rds
2025-10-24 20:33:35.423962 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:33:35.453436 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:33:35.481165 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:33:35.489098 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:33:35.501225 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:33:35.527819 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:33:35.529777 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:33:35.547777 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:33:35.580602 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:33:35.582596 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:33:35.599765 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:33:35.61355 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:33:35.617911 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:33:35.63197 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:33:35.656578 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:33:40.724109 WARNING::Fitting problem for feature 50 returning NA
2025-10-24 20:33:40.750118 WARNING::Fitting problem for feature 62 returning NA
2025-10-24 20:33:40.775025 WARNING::Fitting problem for feature 74 returning NA
2025-10-24 20:33:40.782419 WARNING::Fitting problem for feature 78 returning NA
2025-10-24 20:33:40.793963 WARNING::Fitting problem for feature 84 returning NA
2025-10-24 20:33:40.819253 WARNING::Fitting problem for feature 96 returning NA
2025-10-24 20:33:40.821209 WARNING::Fitting problem for feature 97 returning NA
2025-10-24 20:33:40.825247 WARNING::Fitting problem for feature 99 returning NA
2025-10-24 20:33:40.857165 WARNING::Fitting problem for feature 114 returning NA
2025-10-24 20:33:40.859174 WARNING::Fitting problem for feature 115 returning NA
2025-10-24 20:33:40.875868 WARNING::Fitting problem for feature 123 returning NA
2025-10-24 20:33:40.889745 WARNING::Fitting problem for feature 130 returning NA
2025-10-24 20:33:40.893831 WARNING::Fitting problem for feature 132 returning NA
2025-10-24 20:33:40.907315 WARNING::Fitting problem for feature 139 returning NA
2025-10-24 20:33:40.930424 WARNING::Fitting problem for feature 150 returning NA
2025-10-24 20:33:41.023503 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_linear.rds
2025-10-24 20:33:41.056051 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_linear.rds
2025-10-24 20:33:41.089787 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/residuals_logistic.rds
2025-10-24 20:33:41.258366 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d36beaed7a/fits/fitted_logistic.rds
2025-10-24 20:33:49.052363 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-24 20:33:49.057736 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-24 20:33:49.061391 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-24 20:33:49.077957 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-10-24 20:33:49.083445 ERROR::Effect name not found in metadata: d
2025-10-24 20:33:49.08703 ERROR::No user formula provided
2025-10-24 20:33:49.096366 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-24 20:33:49.100088 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-10-24 20:33:50.174297 INFO::Writing function arguments to log file
2025-10-24 20:33:50.179601 INFO::Verifying options selected are valid
2025-10-24 20:33:51.044608 INFO::Writing function arguments to log file
2025-10-24 20:33:51.049081 INFO::Verifying options selected are valid
2025-10-24 20:33:51.04943 INFO::Determining format of input files
2025-10-24 20:33:51.049726 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 20:33:51.05049 INFO::Running selected normalization method: TSS
2025-10-24 20:33:51.050979 INFO::Creating output feature tables folder
2025-10-24 20:33:51.051352 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/features/data_norm.tsv
2025-10-24 20:33:51.051907 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-24 20:33:51.052197 INFO::Total samples in data: 16
2025-10-24 20:33:51.052467 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-24 20:33:51.052734 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-24 20:33:51.053344 INFO::Total filtered features: 0
2025-10-24 20:33:51.053658 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-24 20:33:51.054018 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-24 20:33:51.054303 INFO::Filtered feature names from variance filtering:
2025-10-24 20:33:51.054578 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/features/filtered_data.tsv
2025-10-24 20:33:51.055077 INFO::Running selected transform method: LOG
2025-10-24 20:33:51.055452 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/features/data_transformed.tsv
2025-10-24 20:33:51.055997 INFO::Applying z-score to standardize continuous metadata
2025-10-24 20:33:51.057848 INFO::Running the linear model component
2025-10-24 20:33:51.06274 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:51.064197 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:51.065525 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:51.067854 INFO::Counting total values for each feature
2025-10-24 20:33:51.068492 INFO::Running the logistic model component
2025-10-24 20:33:51.073197 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:51.0752 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:51.077035 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:51.079801 INFO::Counting total values for each feature
2025-10-24 20:33:51.080547 INFO::Re-running abundances for warn_prevalence
2025-10-24 20:33:51.08092 INFO::Running selected normalization method: TSS
2025-10-24 20:33:51.08141 INFO::Running selected transform method: LOG
2025-10-24 20:33:51.086232 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:51.087588 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:51.08884 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:51.114513 INFO::Creating fits folder
2025-10-24 20:33:51.115074 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/fits/residuals_linear.rds
2025-10-24 20:33:51.115576 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/fits/fitted_linear.rds
2025-10-24 20:33:51.116024 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/fits/residuals_logistic.rds
2025-10-24 20:33:51.116456 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/fits/fitted_logistic.rds
2025-10-24 20:33:51.117364 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/all_results.tsv
2025-10-24 20:33:51.118045 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//RtmpPeoUaM/filee8d310326c54/significant_results.tsv
2025-10-24 20:33:51.118551 INFO::Creating output figures folder
2025-10-24 20:33:51.119026 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/figures/summary_plot.pdf
2025-10-24 20:33:51.706718 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/figures
2025-10-24 20:33:51.707524 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 20:33:51.709543 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 20:33:51.905403 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/figures/summary_plot.pdf
2025-10-24 20:33:52.51761 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d310326c54/figures
2025-10-24 20:33:52.518314 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 20:33:52.520386 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 20:33:52.716269 INFO::Running the linear model component
2025-10-24 20:33:52.719132 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:52.72062 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:52.721838 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:52.724194 INFO::Counting total values for each feature
2025-10-24 20:33:52.724754 INFO::Running the logistic model component
2025-10-24 20:33:52.727374 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:52.729384 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:52.731166 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:52.733907 INFO::Counting total values for each feature
2025-10-24 20:33:52.734562 INFO::Re-running abundances for warn_prevalence
2025-10-24 20:33:52.734791 INFO::Running selected normalization method: TSS
2025-10-24 20:33:52.735233 INFO::Running selected transform method: LOG
2025-10-24 20:33:52.737823 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:52.739116 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:52.740275 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:52.768401 INFO::Creating output folder
2025-10-24 20:33:52.768835 INFO::Creating output figures folder
2025-10-24 20:33:52.769258 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d317cf5269/figures/summary_plot.pdf
2025-10-24 20:33:53.370089 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d317cf5269/figures
2025-10-24 20:33:53.370718 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-24 20:33:53.372702 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-24 20:33:53.764989 INFO::Applying z-score to standardize continuous metadata
2025-10-24 20:33:53.767773 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-24 20:33:53.768061 INFO::Bypass z-score application to metadata
2025-10-24 20:33:53.768806 INFO::Bypass z-score application to metadata
2025-10-24 20:33:53.775848 INFO::Determining format of input files
2025-10-24 20:33:53.776199 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 20:33:53.776458 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-24 20:33:53.778709 INFO::Determining format of input files
2025-10-24 20:33:53.779065 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-24 20:33:53.779456 INFO::Input format is feature_specific_covariate samples as columns
2025-10-24 20:33:53.781895 INFO::Determining format of input files
2025-10-24 20:33:53.782192 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-24 20:33:53.782502 INFO::Input format is feature_specific_covariate samples as columns
2025-10-24 20:33:53.782971 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-24 20:33:53.783195 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-24 20:33:53.786958 INFO::Running selected transform method: LOG
2025-10-24 20:33:53.787344 INFO::Creating output feature tables folder
2025-10-24 20:33:53.787744 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d355280f5e/features/data_transformed.tsv
2025-10-24 20:33:53.789196 INFO::Running selected transform method: LOG
2025-10-24 20:33:53.78957 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d355280f5e/features/data_transformed.tsv
2025-10-24 20:33:53.790909 INFO::Running selected transform method: PLOG
2025-10-24 20:33:53.791413 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d355280f5e/features/data_transformed.tsv
2025-10-24 20:33:53.792315 INFO::Running selected transform method: NONE
2025-10-24 20:33:53.792552 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d355280f5e/features/data_transformed.tsv
2025-10-24 20:33:53.795463 INFO::Running the linear model component
2025-10-24 20:33:53.798156 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:53.799623 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:53.800886 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:53.803323 INFO::Counting total values for each feature
2025-10-24 20:33:53.803886 INFO::Running the logistic model component
2025-10-24 20:33:53.806581 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:53.808699 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:53.810557 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:53.813526 INFO::Counting total values for each feature
2025-10-24 20:33:53.814229 INFO::Re-running abundances for warn_prevalence
2025-10-24 20:33:53.814462 INFO::Running selected normalization method: TSS
2025-10-24 20:33:53.814889 INFO::Running selected transform method: LOG
2025-10-24 20:33:53.817588 INFO::Fitting model to feature number 1, a
2025-10-24 20:33:53.818983 INFO::Fitting model to feature number 2, b
2025-10-24 20:33:53.820255 INFO::Fitting model to feature number 3, c
2025-10-24 20:33:53.849746 INFO::Creating output folder
2025-10-24 20:33:53.850152 INFO::Creating fits folder
2025-10-24 20:33:53.850442 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d339090fff/fits/residuals_linear.rds
2025-10-24 20:33:53.850893 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d339090fff/fits/fitted_linear.rds
2025-10-24 20:33:53.851281 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d339090fff/fits/residuals_logistic.rds
2025-10-24 20:33:53.851657 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d339090fff/fits/fitted_logistic.rds
2025-10-24 20:33:53.852557 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpPeoUaM/filee8d339090fff/all_results.tsv
2025-10-24 20:33:53.853442 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//RtmpPeoUaM/filee8d339090fff/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
136.254   5.283 142.474

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.0230.5288.582
maaslin_check_arguments0.0610.0020.064
maaslin_check_formula0.0650.0070.072
maaslin_compute_formula0.0600.0040.064
maaslin_contrast_test7.1930.6447.941
maaslin_filter0.2230.0130.238
maaslin_fit4.9470.6455.615
maaslin_log_arguments0.0540.0030.057
maaslin_normalize0.1260.0110.137
maaslin_plot_results16.036 0.69816.811
maaslin_plot_results_from_output16.308 0.72117.089
maaslin_process_metadata0.2160.0150.232
maaslin_read_data0.0500.0030.053
maaslin_reorder_data0.0520.0030.054
maaslin_transform0.2840.0300.316
maaslin_write_results5.4320.5375.990
maaslin_write_results_lefse_format5.8630.5276.431
preprocess_dna_mtx0.0020.0000.001
preprocess_taxa_mtx0.0010.0000.002