William Nickols
| Snapshot Date: 2026-03-31 13:40 -0400 (Tue, 31 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 2026-04-01 13:06 -0400 (Wed, 01 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4816 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4539 |
| 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 1178/2374 | 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: 2026-03-31 20:03:52 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 20:07:49 -0400 (Tue, 31 Mar 2026) |
| EllapsedTime: 237.8 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 version 4.6.0 alpha (2026-03-28 r89739)
* 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 Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-01 00:03:52 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 16.886 0.614 17.615
maaslin_plot_results 16.597 0.611 17.378
maaslin_contrast_test 7.119 0.733 7.946
maaslin3 6.978 0.746 7.775
maaslin_write_results 5.916 0.523 6.487
maaslin_write_results_lefse_format 5.813 0.420 6.293
maaslin_fit 5.026 0.463 5.552
* 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 version 4.6.0 alpha (2026-03-28 r89739)
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")
2026-03-31 20:05:29.41 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:05:29.44 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:05:29.47 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:05:29.48 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:05:29.50 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:05:29.53 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:05:29.53 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:05:29.54 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:05:29.57 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:05:29.58 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:05:29.60 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:05:29.61 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:05:29.62 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:05:29.64 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:05:29.67 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:05:35.07 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:05:35.10 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:05:35.13 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:05:35.14 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:05:35.15 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:05:35.18 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:05:35.19 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:05:35.19 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:05:35.23 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:05:35.24 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:05:35.26 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:05:35.28 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:05:35.28 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:05:35.30 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:05:35.32 WARNING::Fitting problem for feature 150 returning NA
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-31 20:05:46.28 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:05:46.32 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:05:46.35 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:05:46.36 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:05:46.37 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:05:46.40 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:05:46.40 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:05:46.41 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:05:46.44 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:05:46.45 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:05:46.46 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:05:46.48 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:05:46.49 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:05:46.51 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:05:46.53 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:05:51.93 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:05:51.96 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:05:52.00 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:05:52.01 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:05:52.03 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:05:52.06 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:05:52.07 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:05:52.07 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:05:52.11 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:05:52.11 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:05:52.13 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:05:52.15 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:05:52.16 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:05:52.18 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:05:52.20 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:05:52.28 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/residuals_linear.rds
2026-03-31 20:05:52.32 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/fitted_linear.rds
2026-03-31 20:05:52.35 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/residuals_logistic.rds
2026-03-31 20:05:52.51 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/fitted_logistic.rds
2026-03-31 20:06:01.17 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:06:01.20 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:06:01.23 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:06:01.24 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:06:01.25 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:06:01.28 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:06:01.28 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:06:01.29 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:06:01.33 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:06:01.33 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:06:01.35 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:06:01.36 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:06:01.37 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:06:01.39 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:06:01.90 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:06:06.57 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:06:06.60 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:06:06.63 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:06:06.64 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:06:06.65 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:06:06.69 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:06:06.70 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:06:06.70 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:06:06.74 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:06:06.74 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:06:06.76 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:06:06.78 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:06:06.78 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:06:06.80 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:06:06.82 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:06:06.89 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/residuals_linear.rds
2026-03-31 20:06:06.93 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/fitted_linear.rds
2026-03-31 20:06:06.98 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/residuals_logistic.rds
2026-03-31 20:06:07.17 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/fitted_logistic.rds
2026-03-31 20:06:15.19 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:06:15.22 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:06:15.25 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:06:15.26 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:06:15.28 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:06:15.31 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:06:15.31 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:06:15.32 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:06:15.36 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:06:15.36 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:06:15.38 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:06:15.39 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:06:15.40 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:06:15.43 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:06:15.45 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:06:20.24 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:06:20.27 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:06:20.30 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:06:20.31 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:06:20.35 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:06:20.38 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:06:20.38 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:06:20.39 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:06:20.43 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:06:20.43 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:06:20.45 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:06:20.46 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:06:20.47 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:06:20.48 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:06:20.51 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:06:20.58 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/residuals_linear.rds
2026-03-31 20:06:20.61 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/fitted_linear.rds
2026-03-31 20:06:20.65 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/residuals_logistic.rds
2026-03-31 20:06:20.82 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605fcb6989/fits/fitted_logistic.rds
2026-03-31 20:06:28.52 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:06:28.54 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:06:28.58 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:06:28.59 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:06:28.60 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:06:28.63 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:06:28.63 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:06:28.64 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:06:28.68 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:06:28.68 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:06:28.70 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:06:28.72 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:06:28.73 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:06:28.74 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:06:28.77 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:06:33.68 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:06:33.71 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:06:33.74 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:06:33.75 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:06:33.76 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:06:33.79 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:06:33.80 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:06:33.80 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:06:33.84 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:06:33.84 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:06:33.87 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:06:33.89 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:06:33.90 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:06:33.91 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:06:33.94 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:06:43.14 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:06:46.73 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:06:55.87 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:06:58.95 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:06:59.15 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_linear.rds
2026-03-31 20:06:59.19 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_linear.rds
2026-03-31 20:06:59.21 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_logistic.rds
2026-03-31 20:06:59.25 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_logistic.rds
2026-03-31 20:07:07.72 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:07:10.25 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:07:10.36 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_linear.rds
2026-03-31 20:07:10.40 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_linear.rds
2026-03-31 20:07:10.42 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_logistic.rds
2026-03-31 20:07:10.46 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_logistic.rds
2026-03-31 20:07:17.28 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:07:19.84 WARNING::Fitting problem for feature 124 returning NA
2026-03-31 20:07:19.96 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_linear.rds
2026-03-31 20:07:20.00 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_linear.rds
2026-03-31 20:07:20.03 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_logistic.rds
2026-03-31 20:07:20.07 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_logistic.rds
2026-03-31 20:07:26.87 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:07:26.90 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:07:26.93 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:07:26.94 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:07:26.96 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:07:26.99 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:07:27.00 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:07:27.00 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:07:27.04 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:07:27.04 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:07:27.06 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:07:27.08 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:07:27.08 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:07:27.10 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:07:27.20 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:07:32.39 WARNING::Fitting problem for feature 50 returning NA
2026-03-31 20:07:32.42 WARNING::Fitting problem for feature 62 returning NA
2026-03-31 20:07:32.46 WARNING::Fitting problem for feature 74 returning NA
2026-03-31 20:07:32.47 WARNING::Fitting problem for feature 78 returning NA
2026-03-31 20:07:32.50 WARNING::Fitting problem for feature 84 returning NA
2026-03-31 20:07:32.53 WARNING::Fitting problem for feature 96 returning NA
2026-03-31 20:07:32.53 WARNING::Fitting problem for feature 97 returning NA
2026-03-31 20:07:32.54 WARNING::Fitting problem for feature 99 returning NA
2026-03-31 20:07:32.60 WARNING::Fitting problem for feature 114 returning NA
2026-03-31 20:07:32.60 WARNING::Fitting problem for feature 115 returning NA
2026-03-31 20:07:32.62 WARNING::Fitting problem for feature 123 returning NA
2026-03-31 20:07:32.64 WARNING::Fitting problem for feature 130 returning NA
2026-03-31 20:07:32.65 WARNING::Fitting problem for feature 132 returning NA
2026-03-31 20:07:32.66 WARNING::Fitting problem for feature 139 returning NA
2026-03-31 20:07:32.69 WARNING::Fitting problem for feature 150 returning NA
2026-03-31 20:07:32.79 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_linear.rds
2026-03-31 20:07:32.82 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_linear.rds
2026-03-31 20:07:32.87 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/residuals_logistic.rds
2026-03-31 20:07:33.04 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e607259bb63/fits/fitted_logistic.rds
2026-03-31 20:07:40.60 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-31 20:07:40.60 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-31 20:07:40.61 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-31 20:07:40.63 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-31 20:07:40.63 ERROR::Effect name not found in metadata: d
2026-03-31 20:07:40.64 ERROR::No user formula provided
2026-03-31 20:07:40.65 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-31 20:07:40.66 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-31 20:07:41.76 INFO::Writing function arguments to log file
2026-03-31 20:07:41.79 INFO::Verifying options selected are valid
2026-03-31 20:07:42.64 INFO::Writing function arguments to log file
2026-03-31 20:07:42.66 INFO::Verifying options selected are valid
2026-03-31 20:07:42.66 INFO::Determining format of input files
2026-03-31 20:07:42.66 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 20:07:42.66 INFO::Running selected normalization method: TSS
2026-03-31 20:07:42.67 INFO::Creating output feature tables folder
2026-03-31 20:07:42.67 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/features/data_norm.tsv
2026-03-31 20:07:42.67 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-31 20:07:42.67 INFO::Total samples in data: 16
2026-03-31 20:07:42.67 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-31 20:07:42.68 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-31 20:07:42.68 INFO::Total filtered features: 0
2026-03-31 20:07:42.68 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-31 20:07:42.68 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-31 20:07:42.68 INFO::Filtered feature names from variance filtering:
2026-03-31 20:07:42.69 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/features/filtered_data.tsv
2026-03-31 20:07:42.69 INFO::Running selected transform method: LOG
2026-03-31 20:07:42.69 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/features/data_transformed.tsv
2026-03-31 20:07:42.69 INFO::Applying z-score to standardize continuous metadata
2026-03-31 20:07:42.69 INFO::Running the linear model component
2026-03-31 20:07:42.72 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:42.72 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:42.72 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:42.72 INFO::Counting total values for each feature
2026-03-31 20:07:42.73 INFO::Running the logistic model component
2026-03-31 20:07:42.75 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:42.75 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:42.75 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:42.76 INFO::Counting total values for each feature
2026-03-31 20:07:42.76 INFO::Re-running abundances for warn_prevalence
2026-03-31 20:07:42.76 INFO::Running selected normalization method: TSS
2026-03-31 20:07:42.76 INFO::Running selected transform method: LOG
2026-03-31 20:07:42.79 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:42.79 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:42.80 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:42.82 INFO::Creating fits folder
2026-03-31 20:07:42.82 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/fits/residuals_linear.rds
2026-03-31 20:07:42.83 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/fits/fitted_linear.rds
2026-03-31 20:07:42.83 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/fits/residuals_logistic.rds
2026-03-31 20:07:42.83 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/fits/fitted_logistic.rds
2026-03-31 20:07:42.83 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/all_results.tsv
2026-03-31 20:07:42.83 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//RtmpXNELkt/file17e605589c262/significant_results.tsv
2026-03-31 20:07:42.84 INFO::Creating output figures folder
2026-03-31 20:07:42.84 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/figures/summary_plot.pdf
2026-03-31 20:07:43.42 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/figures
2026-03-31 20:07:43.42 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-31 20:07:43.42 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-31 20:07:43.61 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/figures/summary_plot.pdf
2026-03-31 20:07:44.19 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e605589c262/figures
2026-03-31 20:07:44.20 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-31 20:07:44.20 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-31 20:07:44.46 INFO::Running the linear model component
2026-03-31 20:07:44.47 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:44.47 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:44.48 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:44.48 INFO::Counting total values for each feature
2026-03-31 20:07:44.48 INFO::Running the logistic model component
2026-03-31 20:07:44.49 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:44.49 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:44.49 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:44.50 INFO::Counting total values for each feature
2026-03-31 20:07:44.50 INFO::Re-running abundances for warn_prevalence
2026-03-31 20:07:44.50 INFO::Running selected normalization method: TSS
2026-03-31 20:07:44.50 INFO::Running selected transform method: LOG
2026-03-31 20:07:44.51 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:44.51 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:44.51 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:44.54 INFO::Creating output folder
2026-03-31 20:07:44.54 INFO::Creating output figures folder
2026-03-31 20:07:44.54 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6050fad52/figures/summary_plot.pdf
2026-03-31 20:07:45.12 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6050fad52/figures
2026-03-31 20:07:45.12 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-31 20:07:45.12 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-31 20:07:45.55 INFO::Applying z-score to standardize continuous metadata
2026-03-31 20:07:45.55 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-31 20:07:45.55 INFO::Bypass z-score application to metadata
2026-03-31 20:07:45.55 INFO::Bypass z-score application to metadata
2026-03-31 20:07:45.57 INFO::Determining format of input files
2026-03-31 20:07:45.58 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 20:07:45.58 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-31 20:07:45.58 INFO::Determining format of input files
2026-03-31 20:07:45.58 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-31 20:07:45.58 INFO::Input format is feature_specific_covariate samples as columns
2026-03-31 20:07:45.59 INFO::Determining format of input files
2026-03-31 20:07:45.59 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-31 20:07:45.59 INFO::Input format is feature_specific_covariate samples as columns
2026-03-31 20:07:45.59 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-31 20:07:45.59 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-31 20:07:45.60 INFO::Running selected transform method: LOG
2026-03-31 20:07:45.60 INFO::Creating output feature tables folder
2026-03-31 20:07:45.60 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e603e3fecf9/features/data_transformed.tsv
2026-03-31 20:07:45.60 INFO::Running selected transform method: LOG
2026-03-31 20:07:45.60 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e603e3fecf9/features/data_transformed.tsv
2026-03-31 20:07:45.60 INFO::Running selected transform method: PLOG
2026-03-31 20:07:45.60 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e603e3fecf9/features/data_transformed.tsv
2026-03-31 20:07:45.61 INFO::Running selected transform method: NONE
2026-03-31 20:07:45.61 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e603e3fecf9/features/data_transformed.tsv
2026-03-31 20:07:45.61 INFO::Running the linear model component
2026-03-31 20:07:45.62 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:45.62 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:45.62 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:45.63 INFO::Counting total values for each feature
2026-03-31 20:07:45.63 INFO::Running the logistic model component
2026-03-31 20:07:45.63 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:45.64 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:45.64 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:45.64 INFO::Counting total values for each feature
2026-03-31 20:07:45.64 INFO::Re-running abundances for warn_prevalence
2026-03-31 20:07:45.64 INFO::Running selected normalization method: TSS
2026-03-31 20:07:45.65 INFO::Running selected transform method: LOG
2026-03-31 20:07:45.66 INFO::Fitting model to feature number 1, a
2026-03-31 20:07:45.66 INFO::Fitting model to feature number 2, b
2026-03-31 20:07:45.66 INFO::Fitting model to feature number 3, c
2026-03-31 20:07:45.69 INFO::Creating output folder
2026-03-31 20:07:45.69 INFO::Creating fits folder
2026-03-31 20:07:45.69 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6056deef5c/fits/residuals_linear.rds
2026-03-31 20:07:45.70 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6056deef5c/fits/fitted_linear.rds
2026-03-31 20:07:45.70 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6056deef5c/fits/residuals_logistic.rds
2026-03-31 20:07:45.70 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6056deef5c/fits/fitted_logistic.rds
2026-03-31 20:07:45.70 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXNELkt/file17e6056deef5c/all_results.tsv
2026-03-31 20:07:45.70 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//RtmpXNELkt/file17e6056deef5c/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
133.665 2.760 137.674
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 6.978 | 0.746 | 7.775 | |
| maaslin_check_arguments | 0.054 | 0.002 | 0.056 | |
| maaslin_check_formula | 0.068 | 0.021 | 0.089 | |
| maaslin_compute_formula | 0.081 | 0.022 | 0.104 | |
| maaslin_contrast_test | 7.119 | 0.733 | 7.946 | |
| maaslin_filter | 0.241 | 0.037 | 0.278 | |
| maaslin_fit | 5.026 | 0.463 | 5.552 | |
| maaslin_log_arguments | 0.068 | 0.020 | 0.088 | |
| maaslin_normalize | 0.140 | 0.027 | 0.167 | |
| maaslin_plot_results | 16.597 | 0.611 | 17.378 | |
| maaslin_plot_results_from_output | 16.886 | 0.614 | 17.615 | |
| maaslin_process_metadata | 0.253 | 0.044 | 0.298 | |
| maaslin_read_data | 0.065 | 0.017 | 0.083 | |
| maaslin_reorder_data | 0.066 | 0.021 | 0.087 | |
| maaslin_transform | 0.302 | 0.048 | 0.363 | |
| maaslin_write_results | 5.916 | 0.523 | 6.487 | |
| maaslin_write_results_lefse_format | 5.813 | 0.420 | 6.293 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.002 | |