William Nickols
| Snapshot Date: 2026-03-17 13:40 -0400 (Tue, 17 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: d4f80f8 |
| git_last_commit_date: 2026-02-09 12:23:40 -0400 (Mon, 09 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-18 11:34 -0400 (Wed, 18 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4857 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4060 |
| 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 1175/2367 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
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. |
| Package: maaslin3 |
| Version: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2026-03-17 19:14:35 -0400 (Tue, 17 Mar 2026) |
| EndedAt: 2026-03-17 19:18:55 -0400 (Tue, 17 Mar 2026) |
| EllapsedTime: 259.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-17 23:14:35 UTC
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* 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 ... NOTE
License stub is invalid DCF.
* 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 17.739 0.781 19.408
maaslin_plot_results 17.611 0.820 19.182
maaslin_contrast_test 6.929 0.613 7.800
maaslin3 6.937 0.483 7.741
maaslin_write_results_lefse_format 5.978 0.503 7.319
maaslin_write_results 5.732 0.544 6.763
maaslin_fit 5.093 0.514 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck/00check.log’
for details.
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** 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)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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")
2026-03-17 19:16:18.42 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:16:18.46 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:16:18.50 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:16:18.52 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:16:18.53 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:16:18.56 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:16:18.56 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:16:18.57 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:16:18.61 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:16:18.61 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:16:18.63 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:16:18.65 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:16:18.65 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:16:18.67 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:16:18.70 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:16:24.64 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:16:24.68 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:16:24.71 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:16:24.72 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:16:24.74 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:16:24.77 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:16:24.77 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:16:24.77 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:16:24.81 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:16:24.81 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:16:24.83 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:16:24.85 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:16:24.85 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:16:24.88 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:16:24.90 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:16:26.607 R[16765:178869465] XType: Using static font registry.
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-17 19:16:37.27 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:16:37.29 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:16:37.32 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:16:37.33 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:16:37.77 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:16:37.80 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:16:37.80 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:16:37.81 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:16:37.85 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:16:37.85 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:16:37.87 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:16:37.88 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:16:37.89 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:16:37.90 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:16:37.93 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:16:43.34 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:16:43.37 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:16:43.40 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:16:43.40 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:16:43.42 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:16:43.45 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:16:43.45 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:16:43.46 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:16:43.52 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:16:43.52 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:16:43.54 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:16:43.56 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:16:43.56 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:16:43.58 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:16:43.61 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:16:43.69 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/residuals_linear.rds
2026-03-17 19:16:43.73 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/fitted_linear.rds
2026-03-17 19:16:43.77 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/residuals_logistic.rds
2026-03-17 19:16:43.96 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/fitted_logistic.rds
2026-03-17 19:16:53.49 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:16:53.52 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:16:53.56 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:16:53.56 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:16:53.58 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:16:53.61 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:16:53.61 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:16:53.62 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:16:53.65 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:16:53.66 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:16:53.68 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:16:53.69 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:16:53.70 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:16:53.71 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:16:53.76 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:16:59.41 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:16:59.44 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:16:59.46 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:16:59.47 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:16:59.49 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:16:59.53 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:16:59.53 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:16:59.54 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:16:59.58 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:16:59.58 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:16:59.60 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:16:59.62 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:16:59.63 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:16:59.65 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:16:59.68 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:16:59.77 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/residuals_linear.rds
2026-03-17 19:16:59.81 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/fitted_linear.rds
2026-03-17 19:16:59.84 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/residuals_logistic.rds
2026-03-17 19:17:00.03 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/fitted_logistic.rds
2026-03-17 19:17:08.92 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:17:08.95 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:17:08.98 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:17:08.99 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:17:09.00 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:17:09.03 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:17:09.03 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:17:09.04 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:17:09.08 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:17:09.08 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:17:09.10 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:17:09.12 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:17:09.12 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:17:09.14 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:17:09.17 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:17:14.45 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:17:14.48 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:17:14.50 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:17:14.51 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:17:14.52 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:17:14.55 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:17:14.56 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:17:14.56 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:17:14.60 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:17:14.60 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:17:14.63 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:17:14.64 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:17:14.65 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:17:14.66 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:17:14.69 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:17:14.79 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/residuals_linear.rds
2026-03-17 19:17:14.83 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/fitted_linear.rds
2026-03-17 19:17:14.86 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/residuals_logistic.rds
2026-03-17 19:17:15.04 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d3cf5b5cf/fits/fitted_logistic.rds
2026-03-17 19:17:24.35 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:17:24.38 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:17:24.41 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:17:24.42 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:17:24.44 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:17:24.47 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:17:24.48 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:17:24.48 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:17:24.52 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:17:24.52 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:17:24.54 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:17:24.56 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:17:24.56 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:17:24.58 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:17:24.62 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:17:29.39 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:17:29.42 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:17:29.45 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:17:29.46 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:17:29.47 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:17:29.50 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:17:29.50 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:17:29.51 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:17:29.55 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:17:29.55 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:17:29.59 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:17:29.61 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:17:29.61 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:17:29.63 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:17:29.66 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:17:39.71 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:17:43.82 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:17:54.26 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:17:57.85 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:17:58.08 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_linear.rds
2026-03-17 19:17:58.12 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_linear.rds
2026-03-17 19:17:58.14 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_logistic.rds
2026-03-17 19:17:58.19 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_logistic.rds
2026-03-17 19:18:08.95 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:18:11.09 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:18:11.22 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_linear.rds
2026-03-17 19:18:11.25 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_linear.rds
2026-03-17 19:18:11.27 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_logistic.rds
2026-03-17 19:18:11.32 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_logistic.rds
2026-03-17 19:18:19.42 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:18:22.18 WARNING::Fitting problem for feature 124 returning NA
2026-03-17 19:18:22.28 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_linear.rds
2026-03-17 19:18:22.32 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_linear.rds
2026-03-17 19:18:22.34 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_logistic.rds
2026-03-17 19:18:22.39 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_logistic.rds
2026-03-17 19:18:30.30 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:18:30.41 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:18:30.44 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:18:30.45 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:18:30.46 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:18:30.49 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:18:30.49 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:18:30.50 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:18:30.53 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:18:30.53 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:18:30.55 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:18:30.57 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:18:30.57 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:18:30.59 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:18:30.62 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:18:36.03 WARNING::Fitting problem for feature 50 returning NA
2026-03-17 19:18:36.06 WARNING::Fitting problem for feature 62 returning NA
2026-03-17 19:18:36.09 WARNING::Fitting problem for feature 74 returning NA
2026-03-17 19:18:36.10 WARNING::Fitting problem for feature 78 returning NA
2026-03-17 19:18:36.12 WARNING::Fitting problem for feature 84 returning NA
2026-03-17 19:18:36.15 WARNING::Fitting problem for feature 96 returning NA
2026-03-17 19:18:36.15 WARNING::Fitting problem for feature 97 returning NA
2026-03-17 19:18:36.16 WARNING::Fitting problem for feature 99 returning NA
2026-03-17 19:18:36.23 WARNING::Fitting problem for feature 114 returning NA
2026-03-17 19:18:36.23 WARNING::Fitting problem for feature 115 returning NA
2026-03-17 19:18:36.25 WARNING::Fitting problem for feature 123 returning NA
2026-03-17 19:18:36.26 WARNING::Fitting problem for feature 130 returning NA
2026-03-17 19:18:36.27 WARNING::Fitting problem for feature 132 returning NA
2026-03-17 19:18:36.29 WARNING::Fitting problem for feature 139 returning NA
2026-03-17 19:18:36.32 WARNING::Fitting problem for feature 150 returning NA
2026-03-17 19:18:36.41 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_linear.rds
2026-03-17 19:18:36.44 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_linear.rds
2026-03-17 19:18:36.48 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/residuals_logistic.rds
2026-03-17 19:18:36.66 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d241362ce/fits/fitted_logistic.rds
2026-03-17 19:18:45.31 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-17 19:18:45.31 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-17 19:18:45.32 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-17 19:18:45.34 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-17 19:18:45.34 ERROR::Effect name not found in metadata: d
2026-03-17 19:18:45.35 ERROR::No user formula provided
2026-03-17 19:18:45.36 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-17 19:18:45.36 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-17 19:18:46.52 INFO::Writing function arguments to log file
2026-03-17 19:18:46.53 INFO::Verifying options selected are valid
2026-03-17 19:18:47.48 INFO::Writing function arguments to log file
2026-03-17 19:18:47.49 INFO::Verifying options selected are valid
2026-03-17 19:18:47.49 INFO::Determining format of input files
2026-03-17 19:18:47.49 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-17 19:18:47.49 INFO::Running selected normalization method: TSS
2026-03-17 19:18:47.49 INFO::Creating output feature tables folder
2026-03-17 19:18:47.49 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/features/data_norm.tsv
2026-03-17 19:18:47.49 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-17 19:18:47.49 INFO::Total samples in data: 16
2026-03-17 19:18:47.49 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-17 19:18:47.49 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-17 19:18:47.50 INFO::Total filtered features: 0
2026-03-17 19:18:47.50 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-17 19:18:47.50 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-17 19:18:47.50 INFO::Filtered feature names from variance filtering:
2026-03-17 19:18:47.50 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/features/filtered_data.tsv
2026-03-17 19:18:47.50 INFO::Running selected transform method: LOG
2026-03-17 19:18:47.50 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/features/data_transformed.tsv
2026-03-17 19:18:47.50 INFO::Applying z-score to standardize continuous metadata
2026-03-17 19:18:47.50 INFO::Running the linear model component
2026-03-17 19:18:47.51 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:47.51 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:47.52 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:47.52 INFO::Counting total values for each feature
2026-03-17 19:18:47.52 INFO::Running the logistic model component
2026-03-17 19:18:47.53 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:47.53 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:47.53 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:47.53 INFO::Counting total values for each feature
2026-03-17 19:18:47.54 INFO::Re-running abundances for warn_prevalence
2026-03-17 19:18:47.54 INFO::Running selected normalization method: TSS
2026-03-17 19:18:47.54 INFO::Running selected transform method: LOG
2026-03-17 19:18:47.54 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:47.55 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:47.55 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:47.58 INFO::Creating fits folder
2026-03-17 19:18:47.58 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/fits/residuals_linear.rds
2026-03-17 19:18:47.58 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/fits/fitted_linear.rds
2026-03-17 19:18:47.58 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/fits/residuals_logistic.rds
2026-03-17 19:18:47.58 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/fits/fitted_logistic.rds
2026-03-17 19:18:47.59 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/all_results.tsv
2026-03-17 19:18:47.59 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//Rtmp6XNkSZ/file417d16423e6c/significant_results.tsv
2026-03-17 19:18:47.59 INFO::Creating output figures folder
2026-03-17 19:18:47.59 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/figures/summary_plot.pdf
2026-03-17 19:18:48.27 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/figures
2026-03-17 19:18:48.27 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-17 19:18:48.27 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-17 19:18:48.54 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/figures/summary_plot.pdf
2026-03-17 19:18:49.22 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d16423e6c/figures
2026-03-17 19:18:49.22 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-17 19:18:49.22 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-17 19:18:49.45 INFO::Running the linear model component
2026-03-17 19:18:49.45 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:49.46 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:49.46 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:49.46 INFO::Counting total values for each feature
2026-03-17 19:18:49.46 INFO::Running the logistic model component
2026-03-17 19:18:49.46 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:49.47 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:49.47 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:49.48 INFO::Counting total values for each feature
2026-03-17 19:18:49.48 INFO::Re-running abundances for warn_prevalence
2026-03-17 19:18:49.48 INFO::Running selected normalization method: TSS
2026-03-17 19:18:49.48 INFO::Running selected transform method: LOG
2026-03-17 19:18:49.48 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:49.48 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:49.48 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:49.51 INFO::Creating output folder
2026-03-17 19:18:49.51 INFO::Creating output figures folder
2026-03-17 19:18:49.51 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d101d1921/figures/summary_plot.pdf
2026-03-17 19:18:50.20 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d101d1921/figures
2026-03-17 19:18:50.20 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-17 19:18:50.20 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-17 19:18:50.67 INFO::Applying z-score to standardize continuous metadata
2026-03-17 19:18:50.68 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-17 19:18:50.68 INFO::Bypass z-score application to metadata
2026-03-17 19:18:50.68 INFO::Bypass z-score application to metadata
2026-03-17 19:18:50.70 INFO::Determining format of input files
2026-03-17 19:18:50.70 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-17 19:18:50.70 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-17 19:18:50.70 INFO::Determining format of input files
2026-03-17 19:18:50.71 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-17 19:18:50.71 INFO::Input format is feature_specific_covariate samples as columns
2026-03-17 19:18:50.71 INFO::Determining format of input files
2026-03-17 19:18:50.71 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-17 19:18:50.71 INFO::Input format is feature_specific_covariate samples as columns
2026-03-17 19:18:50.71 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-17 19:18:50.71 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-17 19:18:50.72 INFO::Running selected transform method: LOG
2026-03-17 19:18:50.72 INFO::Creating output feature tables folder
2026-03-17 19:18:50.72 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d17a41159/features/data_transformed.tsv
2026-03-17 19:18:50.72 INFO::Running selected transform method: LOG
2026-03-17 19:18:50.72 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d17a41159/features/data_transformed.tsv
2026-03-17 19:18:50.72 INFO::Running selected transform method: PLOG
2026-03-17 19:18:50.72 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d17a41159/features/data_transformed.tsv
2026-03-17 19:18:50.72 INFO::Running selected transform method: NONE
2026-03-17 19:18:50.72 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d17a41159/features/data_transformed.tsv
2026-03-17 19:18:50.73 INFO::Running the linear model component
2026-03-17 19:18:50.73 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:50.73 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:50.73 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:50.73 INFO::Counting total values for each feature
2026-03-17 19:18:50.74 INFO::Running the logistic model component
2026-03-17 19:18:50.74 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:50.74 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:50.74 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:50.75 INFO::Counting total values for each feature
2026-03-17 19:18:50.75 INFO::Re-running abundances for warn_prevalence
2026-03-17 19:18:50.75 INFO::Running selected normalization method: TSS
2026-03-17 19:18:50.75 INFO::Running selected transform method: LOG
2026-03-17 19:18:50.75 INFO::Fitting model to feature number 1, a
2026-03-17 19:18:50.75 INFO::Fitting model to feature number 2, b
2026-03-17 19:18:50.76 INFO::Fitting model to feature number 3, c
2026-03-17 19:18:50.80 INFO::Creating output folder
2026-03-17 19:18:50.80 INFO::Creating fits folder
2026-03-17 19:18:50.80 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d146ef62f/fits/residuals_linear.rds
2026-03-17 19:18:50.80 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d146ef62f/fits/fitted_linear.rds
2026-03-17 19:18:50.80 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d146ef62f/fits/residuals_logistic.rds
2026-03-17 19:18:50.80 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d146ef62f/fits/fitted_logistic.rds
2026-03-17 19:18:50.80 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6XNkSZ/file417d146ef62f/all_results.tsv
2026-03-17 19:18:50.80 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//Rtmp6XNkSZ/file417d146ef62f/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
143.478 4.454 153.944
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 6.937 | 0.483 | 7.741 | |
| maaslin_check_arguments | 0.055 | 0.001 | 0.057 | |
| maaslin_check_formula | 0.061 | 0.003 | 0.067 | |
| maaslin_compute_formula | 0.074 | 0.004 | 0.084 | |
| maaslin_contrast_test | 6.929 | 0.613 | 7.800 | |
| maaslin_filter | 0.242 | 0.025 | 0.271 | |
| maaslin_fit | 5.093 | 0.514 | 5.823 | |
| maaslin_log_arguments | 0.066 | 0.003 | 0.072 | |
| maaslin_normalize | 0.137 | 0.010 | 0.150 | |
| maaslin_plot_results | 17.611 | 0.820 | 19.182 | |
| maaslin_plot_results_from_output | 17.739 | 0.781 | 19.408 | |
| maaslin_process_metadata | 0.251 | 0.022 | 0.273 | |
| maaslin_read_data | 0.061 | 0.004 | 0.072 | |
| maaslin_reorder_data | 0.063 | 0.003 | 0.071 | |
| maaslin_transform | 0.304 | 0.036 | 0.346 | |
| maaslin_write_results | 5.732 | 0.544 | 6.763 | |
| maaslin_write_results_lefse_format | 5.978 | 0.503 | 7.319 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.002 | 0.000 | 0.001 | |