William Nickols
| Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 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 2026-03-14 11:34 -0400 (Sat, 14 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" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4050 |
| 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 1172/2361 | 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: 2026-03-13 19:10:03 -0400 (Fri, 13 Mar 2026) |
| EndedAt: 2026-03-13 19:14:22 -0400 (Fri, 13 Mar 2026) |
| EllapsedTime: 259.5 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: 2026-03-13 23:10:03 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 17.682 0.793 19.234
maaslin_plot_results 17.433 0.803 18.896
maaslin3 6.999 0.460 8.155
maaslin_contrast_test 6.837 0.556 7.596
maaslin_write_results 5.827 0.579 6.637
maaslin_write_results_lefse_format 5.932 0.447 6.648
maaslin_fit 5.040 0.567 5.919
* 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")
2026-03-13 19:11:45.01 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:11:45.04 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:11:45.07 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:11:45.08 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:11:45.09 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:11:45.13 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:11:45.13 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:11:45.13 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:11:45.17 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:11:45.17 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:11:45.20 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:11:45.22 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:11:45.22 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:11:45.24 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:11:45.26 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:11:51.22 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:11:51.25 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:11:51.28 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:11:51.29 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:11:51.32 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:11:51.35 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:11:51.35 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:11:51.35 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:11:51.39 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:11:51.39 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:11:51.41 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:11:51.43 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:11:51.43 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:11:51.46 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:11:51.49 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:11:53.156 R[68567:152624460] XType: Using static font registry.
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-13 19:12:03.55 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:03.58 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:03.61 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:03.62 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:04.07 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:04.10 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:04.10 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:04.10 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:04.14 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:04.15 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:04.16 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:04.18 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:04.18 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:04.20 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:04.22 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:09.61 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:09.64 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:09.66 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:09.67 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:09.69 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:09.72 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:09.72 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:09.72 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:09.78 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:09.78 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:09.80 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:09.82 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:09.82 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:09.84 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:09.86 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:09.94 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/residuals_linear.rds
2026-03-13 19:12:09.98 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/fitted_linear.rds
2026-03-13 19:12:10.02 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/residuals_logistic.rds
2026-03-13 19:12:10.21 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/fitted_logistic.rds
2026-03-13 19:12:19.80 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:19.83 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:19.87 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:19.87 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:19.89 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:19.92 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:19.93 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:19.93 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:19.97 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:19.97 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:19.99 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:20.00 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:20.01 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:20.02 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:20.07 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:25.69 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:25.72 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:25.75 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:25.76 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:25.77 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:25.80 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:25.81 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:25.81 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:25.85 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:25.85 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:25.87 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:25.89 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:25.90 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:25.92 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:25.94 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:26.04 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/residuals_linear.rds
2026-03-13 19:12:26.08 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/fitted_linear.rds
2026-03-13 19:12:26.12 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/residuals_logistic.rds
2026-03-13 19:12:26.31 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/fitted_logistic.rds
2026-03-13 19:12:35.19 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:35.22 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:35.26 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:35.27 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:35.28 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:35.32 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:35.32 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:35.33 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:35.37 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:35.37 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:35.39 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:35.41 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:35.41 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:35.43 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:35.45 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:41.22 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:41.24 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:41.27 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:41.28 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:41.29 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:41.32 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:41.33 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:41.33 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:41.36 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:41.37 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:41.39 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:41.41 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:41.41 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:41.43 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:41.46 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:41.56 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/residuals_linear.rds
2026-03-13 19:12:41.60 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/fitted_linear.rds
2026-03-13 19:12:41.63 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/residuals_logistic.rds
2026-03-13 19:12:41.82 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd739e187aa/fits/fitted_logistic.rds
2026-03-13 19:12:51.16 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:51.19 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:51.22 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:51.23 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:51.24 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:51.27 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:51.27 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:51.28 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:51.31 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:51.32 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:51.33 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:51.35 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:51.36 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:51.37 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:51.41 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:12:56.04 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:12:56.07 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:12:56.10 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:12:56.11 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:12:56.12 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:12:56.15 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:12:56.15 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:12:56.16 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:12:56.20 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:12:56.20 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:12:56.23 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:12:56.24 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:12:56.25 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:12:56.27 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:12:56.30 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:13:06.33 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:10.46 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:20.92 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:24.65 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:24.87 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_linear.rds
2026-03-13 19:13:24.91 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_linear.rds
2026-03-13 19:13:24.94 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_logistic.rds
2026-03-13 19:13:24.98 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_logistic.rds
2026-03-13 19:13:35.22 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:37.40 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:37.51 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_linear.rds
2026-03-13 19:13:37.55 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_linear.rds
2026-03-13 19:13:37.57 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_logistic.rds
2026-03-13 19:13:37.61 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_logistic.rds
2026-03-13 19:13:45.83 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:48.64 WARNING::Fitting problem for feature 124 returning NA
2026-03-13 19:13:48.75 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_linear.rds
2026-03-13 19:13:48.78 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_linear.rds
2026-03-13 19:13:48.80 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_logistic.rds
2026-03-13 19:13:48.85 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_logistic.rds
2026-03-13 19:13:56.77 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:13:56.81 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:13:56.84 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:13:56.85 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:13:56.86 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:13:56.89 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:13:56.89 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:13:56.90 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:13:56.93 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:13:56.93 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:13:56.95 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:13:56.97 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:13:56.97 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:13:56.99 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:13:57.01 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:14:02.40 WARNING::Fitting problem for feature 50 returning NA
2026-03-13 19:14:02.43 WARNING::Fitting problem for feature 62 returning NA
2026-03-13 19:14:02.46 WARNING::Fitting problem for feature 74 returning NA
2026-03-13 19:14:02.47 WARNING::Fitting problem for feature 78 returning NA
2026-03-13 19:14:02.49 WARNING::Fitting problem for feature 84 returning NA
2026-03-13 19:14:02.52 WARNING::Fitting problem for feature 96 returning NA
2026-03-13 19:14:02.52 WARNING::Fitting problem for feature 97 returning NA
2026-03-13 19:14:02.53 WARNING::Fitting problem for feature 99 returning NA
2026-03-13 19:14:02.59 WARNING::Fitting problem for feature 114 returning NA
2026-03-13 19:14:02.60 WARNING::Fitting problem for feature 115 returning NA
2026-03-13 19:14:02.61 WARNING::Fitting problem for feature 123 returning NA
2026-03-13 19:14:02.63 WARNING::Fitting problem for feature 130 returning NA
2026-03-13 19:14:02.63 WARNING::Fitting problem for feature 132 returning NA
2026-03-13 19:14:02.65 WARNING::Fitting problem for feature 139 returning NA
2026-03-13 19:14:02.67 WARNING::Fitting problem for feature 150 returning NA
2026-03-13 19:14:02.76 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_linear.rds
2026-03-13 19:14:02.80 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_linear.rds
2026-03-13 19:14:02.83 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/residuals_logistic.rds
2026-03-13 19:14:03.01 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd71495d933/fits/fitted_logistic.rds
2026-03-13 19:14:12.29 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-13 19:14:12.30 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-13 19:14:12.30 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-13 19:14:12.33 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-13 19:14:12.33 ERROR::Effect name not found in metadata: d
2026-03-13 19:14:12.34 ERROR::No user formula provided
2026-03-13 19:14:12.35 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-13 19:14:12.36 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-13 19:14:13.50 INFO::Writing function arguments to log file
2026-03-13 19:14:13.51 INFO::Verifying options selected are valid
2026-03-13 19:14:14.46 INFO::Writing function arguments to log file
2026-03-13 19:14:14.46 INFO::Verifying options selected are valid
2026-03-13 19:14:14.47 INFO::Determining format of input files
2026-03-13 19:14:14.47 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-13 19:14:14.47 INFO::Running selected normalization method: TSS
2026-03-13 19:14:14.47 INFO::Creating output feature tables folder
2026-03-13 19:14:14.47 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/features/data_norm.tsv
2026-03-13 19:14:14.47 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-13 19:14:14.47 INFO::Total samples in data: 16
2026-03-13 19:14:14.47 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-13 19:14:14.47 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-13 19:14:14.47 INFO::Total filtered features: 0
2026-03-13 19:14:14.47 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-13 19:14:14.47 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-13 19:14:14.47 INFO::Filtered feature names from variance filtering:
2026-03-13 19:14:14.47 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/features/filtered_data.tsv
2026-03-13 19:14:14.47 INFO::Running selected transform method: LOG
2026-03-13 19:14:14.47 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/features/data_transformed.tsv
2026-03-13 19:14:14.47 INFO::Applying z-score to standardize continuous metadata
2026-03-13 19:14:14.48 INFO::Running the linear model component
2026-03-13 19:14:14.48 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:14.48 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:14.49 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:14.49 INFO::Counting total values for each feature
2026-03-13 19:14:14.49 INFO::Running the logistic model component
2026-03-13 19:14:14.50 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:14.50 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:14.50 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:14.50 INFO::Counting total values for each feature
2026-03-13 19:14:14.51 INFO::Re-running abundances for warn_prevalence
2026-03-13 19:14:14.51 INFO::Running selected normalization method: TSS
2026-03-13 19:14:14.51 INFO::Running selected transform method: LOG
2026-03-13 19:14:14.52 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:14.52 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:14.52 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:14.55 INFO::Creating fits folder
2026-03-13 19:14:14.55 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/fits/residuals_linear.rds
2026-03-13 19:14:14.55 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/fits/fitted_linear.rds
2026-03-13 19:14:14.55 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/fits/residuals_logistic.rds
2026-03-13 19:14:14.55 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/fits/fitted_logistic.rds
2026-03-13 19:14:14.55 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/all_results.tsv
2026-03-13 19:14:14.55 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//RtmpTh11ZD/file10bd7417cff5b/significant_results.tsv
2026-03-13 19:14:14.55 INFO::Creating output figures folder
2026-03-13 19:14:14.55 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/figures/summary_plot.pdf
2026-03-13 19:14:15.20 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/figures
2026-03-13 19:14:15.20 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-13 19:14:15.21 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-13 19:14:15.42 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/figures/summary_plot.pdf
2026-03-13 19:14:16.07 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd7417cff5b/figures
2026-03-13 19:14:16.07 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-13 19:14:16.07 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-13 19:14:16.28 INFO::Running the linear model component
2026-03-13 19:14:16.28 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:16.29 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:16.29 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:16.29 INFO::Counting total values for each feature
2026-03-13 19:14:16.29 INFO::Running the logistic model component
2026-03-13 19:14:16.29 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:16.30 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:16.30 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:16.30 INFO::Counting total values for each feature
2026-03-13 19:14:16.30 INFO::Re-running abundances for warn_prevalence
2026-03-13 19:14:16.30 INFO::Running selected normalization method: TSS
2026-03-13 19:14:16.30 INFO::Running selected transform method: LOG
2026-03-13 19:14:16.30 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:16.30 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:16.31 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:16.33 INFO::Creating output folder
2026-03-13 19:14:16.33 INFO::Creating output figures folder
2026-03-13 19:14:16.33 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd75a0e50cb/figures/summary_plot.pdf
2026-03-13 19:14:16.99 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd75a0e50cb/figures
2026-03-13 19:14:16.99 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-13 19:14:16.99 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-13 19:14:17.43 INFO::Applying z-score to standardize continuous metadata
2026-03-13 19:14:17.43 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-13 19:14:17.43 INFO::Bypass z-score application to metadata
2026-03-13 19:14:17.43 INFO::Bypass z-score application to metadata
2026-03-13 19:14:17.45 INFO::Determining format of input files
2026-03-13 19:14:17.45 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-13 19:14:17.45 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-13 19:14:17.46 INFO::Determining format of input files
2026-03-13 19:14:17.46 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-13 19:14:17.46 INFO::Input format is feature_specific_covariate samples as columns
2026-03-13 19:14:17.46 INFO::Determining format of input files
2026-03-13 19:14:17.46 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-13 19:14:17.46 INFO::Input format is feature_specific_covariate samples as columns
2026-03-13 19:14:17.46 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-13 19:14:17.46 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-13 19:14:17.47 INFO::Running selected transform method: LOG
2026-03-13 19:14:17.47 INFO::Creating output feature tables folder
2026-03-13 19:14:17.47 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd79dbb999/features/data_transformed.tsv
2026-03-13 19:14:17.48 INFO::Running selected transform method: LOG
2026-03-13 19:14:17.48 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd79dbb999/features/data_transformed.tsv
2026-03-13 19:14:17.48 INFO::Running selected transform method: PLOG
2026-03-13 19:14:17.48 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd79dbb999/features/data_transformed.tsv
2026-03-13 19:14:17.48 INFO::Running selected transform method: NONE
2026-03-13 19:14:17.48 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd79dbb999/features/data_transformed.tsv
2026-03-13 19:14:17.48 INFO::Running the linear model component
2026-03-13 19:14:17.49 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:17.49 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:17.49 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:17.49 INFO::Counting total values for each feature
2026-03-13 19:14:17.49 INFO::Running the logistic model component
2026-03-13 19:14:17.50 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:17.50 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:17.50 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:17.50 INFO::Counting total values for each feature
2026-03-13 19:14:17.50 INFO::Re-running abundances for warn_prevalence
2026-03-13 19:14:17.50 INFO::Running selected normalization method: TSS
2026-03-13 19:14:17.50 INFO::Running selected transform method: LOG
2026-03-13 19:14:17.51 INFO::Fitting model to feature number 1, a
2026-03-13 19:14:17.51 INFO::Fitting model to feature number 2, b
2026-03-13 19:14:17.51 INFO::Fitting model to feature number 3, c
2026-03-13 19:14:17.54 INFO::Creating output folder
2026-03-13 19:14:17.54 INFO::Creating fits folder
2026-03-13 19:14:17.54 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd73875f0dd/fits/residuals_linear.rds
2026-03-13 19:14:17.54 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd73875f0dd/fits/fitted_linear.rds
2026-03-13 19:14:17.54 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd73875f0dd/fits/residuals_logistic.rds
2026-03-13 19:14:17.54 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd73875f0dd/fits/fitted_logistic.rds
2026-03-13 19:14:17.54 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpTh11ZD/file10bd73875f0dd/all_results.tsv
2026-03-13 19:14:17.54 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//RtmpTh11ZD/file10bd73875f0dd/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
143.975 4.523 154.031
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 6.999 | 0.460 | 8.155 | |
| maaslin_check_arguments | 0.053 | 0.001 | 0.056 | |
| maaslin_check_formula | 0.061 | 0.006 | 0.067 | |
| maaslin_compute_formula | 0.075 | 0.005 | 0.087 | |
| maaslin_contrast_test | 6.837 | 0.556 | 7.596 | |
| maaslin_filter | 0.249 | 0.032 | 0.302 | |
| maaslin_fit | 5.040 | 0.567 | 5.919 | |
| maaslin_log_arguments | 0.060 | 0.003 | 0.068 | |
| maaslin_normalize | 0.133 | 0.011 | 0.150 | |
| maaslin_plot_results | 17.433 | 0.803 | 18.896 | |
| maaslin_plot_results_from_output | 17.682 | 0.793 | 19.234 | |
| maaslin_process_metadata | 0.238 | 0.026 | 0.275 | |
| maaslin_read_data | 0.058 | 0.003 | 0.061 | |
| maaslin_reorder_data | 0.067 | 0.004 | 0.071 | |
| maaslin_transform | 0.314 | 0.036 | 0.371 | |
| maaslin_write_results | 5.827 | 0.579 | 6.637 | |
| maaslin_write_results_lefse_format | 5.932 | 0.447 | 6.648 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |