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This page was generated on 2025-08-21 12:06 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1147/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 Aug 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: ed6ae28
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on 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: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.1.0.tar.gz
StartedAt: 2025-08-20 20:04:04 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 20:08:33 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 269.2 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   13.904  0.768  15.219
maaslin_plot_results               13.587  0.585  14.271
maaslin3                            8.565  0.490   9.101
maaslin_contrast_test               6.510  0.709   7.250
maaslin_write_results_lefse_format  5.615  0.556   6.237
maaslin_write_results               5.252  0.614   5.933
maaslin_fit                         4.561  0.491   5.060
* 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 ‘1.1.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "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")
2025-08-20 20:06:26.507616 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:06:26.535424 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:06:26.564781 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:06:26.572457 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:06:26.589506 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:06:26.615864 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:06:26.624415 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:06:26.628498 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:06:26.665626 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:06:26.673643 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:06:26.694636 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:06:26.709599 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:06:26.714052 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:06:26.729441 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:06:26.759977 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:06:33.160667 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:06:33.197815 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:06:33.223507 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:06:33.231011 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:06:33.242729 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:06:33.269016 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:06:33.271032 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:06:33.275138 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:06:33.308382 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:06:33.310427 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:06:33.327628 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:06:33.341462 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:06:33.345838 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:06:33.360016 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:06:33.384377 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:06:34.572 R[24272:57069500] XType: Using static font registry.
2025-08-20 20:06:41.1161 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:06:41.143223 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:06:41.178917 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:06:41.186322 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:06:41.207953 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:06:41.2356 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:06:41.2377 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:06:41.242277 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:06:41.273643 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:06:41.275639 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:06:41.292439 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:06:41.306815 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:06:41.312473 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:06:41.327898 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:06:41.372769 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:06:46.945319 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:06:46.970788 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:06:46.995746 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:06:47.003264 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:06:47.01482 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:06:47.04065 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:06:47.042713 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:06:47.046871 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:06:47.082527 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:06:47.084779 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:06:47.103888 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:06:47.119073 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:06:47.123661 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:06:47.139001 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:06:47.164396 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:06:47.253123 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/residuals_linear.rds
2025-08-20 20:06:47.308178 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/fitted_linear.rds
2025-08-20 20:06:47.342899 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/residuals_logistic.rds
2025-08-20 20:06:47.5201 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/fitted_logistic.rds
2025-08-20 20:06:54.834553 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:06:54.864027 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:06:54.890848 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:06:54.898847 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:06:54.911315 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:06:54.939104 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:06:54.941138 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:06:54.945226 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:06:54.978732 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:06:54.980847 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:06:54.99828 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:06:55.012278 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:06:55.016688 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:06:55.031028 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:06:55.055088 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:07:00.329458 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:07:00.355738 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:07:00.381948 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:07:00.389957 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:07:00.403559 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:07:00.434511 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:07:00.436942 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:07:00.442094 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:07:00.500167 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:07:00.50234 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:07:00.519018 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:07:00.532247 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:07:00.538248 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:07:00.551482 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:07:00.576463 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:07:00.64785 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/residuals_linear.rds
2025-08-20 20:07:00.689752 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/fitted_linear.rds
2025-08-20 20:07:00.725791 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/residuals_logistic.rds
2025-08-20 20:07:00.948476 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/fitted_logistic.rds
2025-08-20 20:07:07.792867 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:07:07.819916 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:07:07.84553 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:07:07.853504 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:07:07.865839 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:07:07.89224 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:07:07.894348 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:07:07.89854 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:07:07.933073 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:07:07.935083 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:07:07.952988 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:07:07.966335 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:07:07.970592 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:07:07.985656 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:07:08.009998 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:07:12.832571 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:07:12.859588 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:07:12.885827 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:07:12.893604 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:07:12.906081 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:07:12.935894 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:07:12.938138 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:07:12.942767 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:07:13.001957 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:07:13.004083 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:07:13.021664 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:07:13.035929 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:07:13.040184 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:07:13.053695 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:07:13.07696 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:07:13.144894 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/residuals_linear.rds
2025-08-20 20:07:13.177248 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/fitted_linear.rds
2025-08-20 20:07:13.210332 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/residuals_logistic.rds
2025-08-20 20:07:13.379493 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed047aba528/fits/fitted_logistic.rds
2025-08-20 20:07:19.865999 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:07:19.893549 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:07:19.920198 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:07:19.928519 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:07:19.940718 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:07:19.967923 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:07:19.970099 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:07:19.974452 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:07:20.00871 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:07:20.010785 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:07:20.027632 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:07:20.041809 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:07:20.04623 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:07:20.060741 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:07:20.085419 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:07:25.103835 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:07:25.131046 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:07:25.156731 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:07:25.164715 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:07:25.177108 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:07:25.204598 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:07:25.206714 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:07:25.21096 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:07:25.245172 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:07:25.247275 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:07:25.264559 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:07:25.278852 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:07:25.283597 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:07:25.299214 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:07:25.325922 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:07:32.721792 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:07:36.411007 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:07:44.193671 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:07:47.988137 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:07:48.17308 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_linear.rds
2025-08-20 20:07:48.205805 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_linear.rds
2025-08-20 20:07:48.227957 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_logistic.rds
2025-08-20 20:07:48.26811 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_logistic.rds
2025-08-20 20:07:55.495264 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:07:58.117458 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:07:58.215714 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_linear.rds
2025-08-20 20:07:58.248512 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_linear.rds
2025-08-20 20:07:58.271117 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_logistic.rds
2025-08-20 20:07:58.311254 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_logistic.rds
2025-08-20 20:08:04.217726 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:08:06.415505 WARNING::Fitting problem for feature 124 returning NA
2025-08-20 20:08:06.510613 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_linear.rds
2025-08-20 20:08:06.543475 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_linear.rds
2025-08-20 20:08:06.565365 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_logistic.rds
2025-08-20 20:08:06.604655 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_logistic.rds
2025-08-20 20:08:12.848069 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:08:12.874116 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:08:12.900136 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:08:12.907704 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:08:12.931454 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:08:12.956707 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:08:12.95861 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:08:12.962569 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:08:12.99467 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:08:12.996588 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:08:13.013163 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:08:13.026874 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:08:13.031187 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:08:13.04483 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:08:13.068595 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:08:17.990614 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 20:08:18.017476 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 20:08:18.043659 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 20:08:18.051231 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 20:08:18.063702 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 20:08:18.090571 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 20:08:18.092616 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 20:08:18.096863 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 20:08:18.129232 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 20:08:18.131228 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 20:08:18.147908 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 20:08:18.161475 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 20:08:18.165509 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 20:08:18.17896 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 20:08:18.202881 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 20:08:18.312137 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_linear.rds
2025-08-20 20:08:18.344114 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_linear.rds
2025-08-20 20:08:18.377374 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/residuals_logistic.rds
2025-08-20 20:08:18.545857 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed05b96b22d/fits/fitted_logistic.rds
2025-08-20 20:08:24.735018 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-20 20:08:24.740374 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-20 20:08:24.744156 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-20 20:08:24.760309 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-20 20:08:24.765676 ERROR::Effect name not found in metadata: d
2025-08-20 20:08:24.769174 ERROR::No user formula provided
2025-08-20 20:08:24.778617 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-20 20:08:24.782443 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-20 20:08:25.779041 INFO::Writing function arguments to log file
2025-08-20 20:08:25.784804 INFO::Verifying options selected are valid
2025-08-20 20:08:26.457598 INFO::Writing function arguments to log file
2025-08-20 20:08:26.462341 INFO::Verifying options selected are valid
2025-08-20 20:08:26.462763 INFO::Determining format of input files
2025-08-20 20:08:26.463077 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-20 20:08:26.463894 INFO::Running selected normalization method: TSS
2025-08-20 20:08:26.464405 INFO::Creating output feature tables folder
2025-08-20 20:08:26.464799 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/features/data_norm.tsv
2025-08-20 20:08:26.465385 INFO::Filter data based on min abundance and min prevalence
2025-08-20 20:08:26.465679 INFO::Total samples in data: 16
2025-08-20 20:08:26.465963 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-20 20:08:26.466583 INFO::Total filtered features: 0
2025-08-20 20:08:26.466928 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-20 20:08:26.467297 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-20 20:08:26.467608 INFO::Filtered feature names from variance filtering:
2025-08-20 20:08:26.467899 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/features/filtered_data.tsv
2025-08-20 20:08:26.468457 INFO::Running selected transform method: LOG
2025-08-20 20:08:26.468864 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/features/data_transformed.tsv
2025-08-20 20:08:26.469566 INFO::Applying z-score to standardize continuous metadata
2025-08-20 20:08:26.47171 INFO::Running the linear model component
2025-08-20 20:08:26.477046 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:26.478576 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:26.47989 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:26.482236 INFO::Counting total values for each feature
2025-08-20 20:08:26.482906 INFO::Running the logistic model component
2025-08-20 20:08:26.487917 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:26.49 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:26.491928 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:26.494977 INFO::Counting total values for each feature
2025-08-20 20:08:26.495811 INFO::Re-running abundances for warn_prevalence
2025-08-20 20:08:26.496132 INFO::Running selected normalization method: TSS
2025-08-20 20:08:26.496674 INFO::Running selected transform method: LOG
2025-08-20 20:08:26.502312 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:26.503851 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:26.505246 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:26.533025 INFO::Creating fits folder
2025-08-20 20:08:26.533683 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/fits/residuals_linear.rds
2025-08-20 20:08:26.534187 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/fits/fitted_linear.rds
2025-08-20 20:08:26.534641 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/fits/residuals_logistic.rds
2025-08-20 20:08:26.535122 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/fits/fitted_logistic.rds
2025-08-20 20:08:26.536053 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/all_results.tsv
2025-08-20 20:08:26.536738 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//RtmpMqlw95/file5ed020152665/significant_results.tsv
2025-08-20 20:08:26.537283 INFO::Creating output figures folder
2025-08-20 20:08:26.537773 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/figures/summary_plot.pdf
2025-08-20 20:08:27.012807 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/figures
2025-08-20 20:08:27.013547 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-20 20:08:27.015396 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-20 20:08:27.165647 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/figures/summary_plot.pdf
2025-08-20 20:08:27.630562 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed020152665/figures
2025-08-20 20:08:27.631179 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-20 20:08:27.633049 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-20 20:08:27.777943 INFO::Running the linear model component
2025-08-20 20:08:27.780589 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:27.781942 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:27.783063 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:27.785227 INFO::Counting total values for each feature
2025-08-20 20:08:27.785712 INFO::Running the logistic model component
2025-08-20 20:08:27.787998 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:27.789767 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:27.79135 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:27.793739 INFO::Counting total values for each feature
2025-08-20 20:08:27.794314 INFO::Re-running abundances for warn_prevalence
2025-08-20 20:08:27.79452 INFO::Running selected normalization method: TSS
2025-08-20 20:08:27.79489 INFO::Running selected transform method: LOG
2025-08-20 20:08:27.797234 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:27.798341 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:27.799398 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:27.82358 INFO::Creating output folder
2025-08-20 20:08:27.824012 INFO::Creating output figures folder
2025-08-20 20:08:27.824432 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed0522a4df8/figures/summary_plot.pdf
2025-08-20 20:08:28.264403 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed0522a4df8/figures
2025-08-20 20:08:28.265023 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-20 20:08:28.266751 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-20 20:08:28.588966 INFO::Applying z-score to standardize continuous metadata
2025-08-20 20:08:28.591258 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-20 20:08:28.591487 INFO::Bypass z-score application to metadata
2025-08-20 20:08:28.592124 INFO::Bypass z-score application to metadata
2025-08-20 20:08:28.59783 INFO::Determining format of input files
2025-08-20 20:08:28.598112 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-20 20:08:28.598343 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-20 20:08:28.600322 INFO::Determining format of input files
2025-08-20 20:08:28.600617 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-20 20:08:28.600977 INFO::Input format is feature_specific_covariate samples as columns
2025-08-20 20:08:28.603199 INFO::Determining format of input files
2025-08-20 20:08:28.603458 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-20 20:08:28.603738 INFO::Input format is feature_specific_covariate samples as columns
2025-08-20 20:08:28.604166 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-20 20:08:28.604369 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-20 20:08:28.607545 INFO::Running selected transform method: LOG
2025-08-20 20:08:28.607859 INFO::Creating output feature tables folder
2025-08-20 20:08:28.608193 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed0c9c5922/features/data_transformed.tsv
2025-08-20 20:08:28.609414 INFO::Running selected transform method: LOG
2025-08-20 20:08:28.609724 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed0c9c5922/features/data_transformed.tsv
2025-08-20 20:08:28.610807 INFO::Running selected transform method: PLOG
2025-08-20 20:08:28.611259 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed0c9c5922/features/data_transformed.tsv
2025-08-20 20:08:28.612079 INFO::Running selected transform method: NONE
2025-08-20 20:08:28.612304 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed0c9c5922/features/data_transformed.tsv
2025-08-20 20:08:28.61474 INFO::Running the linear model component
2025-08-20 20:08:28.617184 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:28.618454 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:28.619513 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:28.621615 INFO::Counting total values for each feature
2025-08-20 20:08:28.62212 INFO::Running the logistic model component
2025-08-20 20:08:28.624564 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:28.626525 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:28.628276 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:28.63106 INFO::Counting total values for each feature
2025-08-20 20:08:28.631708 INFO::Re-running abundances for warn_prevalence
2025-08-20 20:08:28.631939 INFO::Running selected normalization method: TSS
2025-08-20 20:08:28.632348 INFO::Running selected transform method: LOG
2025-08-20 20:08:28.634891 INFO::Fitting model to feature number 1, a
2025-08-20 20:08:28.63614 INFO::Fitting model to feature number 2, b
2025-08-20 20:08:28.637301 INFO::Fitting model to feature number 3, c
2025-08-20 20:08:28.662739 INFO::Creating output folder
2025-08-20 20:08:28.663127 INFO::Creating fits folder
2025-08-20 20:08:28.663449 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed06c9fcda5/fits/residuals_linear.rds
2025-08-20 20:08:28.663878 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed06c9fcda5/fits/fitted_linear.rds
2025-08-20 20:08:28.664257 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed06c9fcda5/fits/residuals_logistic.rds
2025-08-20 20:08:28.664622 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed06c9fcda5/fits/fitted_logistic.rds
2025-08-20 20:08:28.665432 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpMqlw95/file5ed06c9fcda5/all_results.tsv
2025-08-20 20:08:28.665981 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//RtmpMqlw95/file5ed06c9fcda5/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
119.767   5.216 127.027

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.5650.4909.101
maaslin_check_arguments0.0520.0010.055
maaslin_check_formula0.0550.0050.059
maaslin_compute_formula0.0550.0040.059
maaslin_contrast_test6.5100.7097.250
maaslin_filter0.5540.0960.652
maaslin_fit4.5610.4915.060
maaslin_log_arguments0.0500.0030.053
maaslin_normalize0.1180.0100.127
maaslin_plot_results13.587 0.58514.271
maaslin_plot_results_from_output13.904 0.76815.219
maaslin_process_metadata0.2220.0420.294
maaslin_read_data0.0510.0040.056
maaslin_reorder_data0.0550.0040.064
maaslin_transform0.2860.0590.363
maaslin_write_results5.2520.6145.933
maaslin_write_results_lefse_format5.6150.5566.237
preprocess_dna_mtx0.0020.0000.001
preprocess_taxa_mtx0.0010.0000.002