William Nickols
| Snapshot Date: 2026-03-03 13:40 -0500 (Tue, 03 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 -0500 (Mon, 09 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-04 11:35 -0500 (Wed, 04 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4882 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4574 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2357 | 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: 2026-03-03 20:36:29 -0500 (Tue, 03 Mar 2026) |
| EndedAt: 2026-03-03 20:40:53 -0500 (Tue, 03 Mar 2026) |
| EllapsedTime: 263.5 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) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* 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 17.241 0.883 19.129
maaslin_plot_results_from_output 17.217 0.703 18.865
maaslin3 7.065 0.468 7.740
maaslin_contrast_test 6.843 0.616 8.028
maaslin_write_results_lefse_format 6.016 0.653 6.984
maaslin_write_results 5.736 0.626 6.747
maaslin_fit 5.073 0.580 5.980
* 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-arm64/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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2026-03-03 20:38:12.78 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:38:12.81 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:38:12.85 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:38:12.86 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:38:12.87 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:38:12.90 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:38:12.91 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:38:12.91 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:38:12.95 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:38:12.95 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:38:12.97 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:38:12.99 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:38:13.00 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:38:13.02 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:38:13.05 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:38:18.95 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:38:18.98 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:38:19.02 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:38:19.03 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:38:19.04 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:38:19.08 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:38:19.08 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:38:19.08 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:38:19.13 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:38:19.13 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:38:19.15 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:38:19.18 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:38:19.19 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:38:19.20 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:38:19.23 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:38:20.991 R[54578:78362431] XType: Using static font registry.
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-03 20:38:32.07 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:38:32.10 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:38:32.13 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:38:32.13 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:38:32.15 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:38:32.18 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:38:32.18 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:38:32.19 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:38:32.23 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:38:32.23 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:38:32.25 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:38:32.27 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:38:32.27 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:38:32.29 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:38:32.32 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:38:37.59 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:38:37.62 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:38:37.65 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:38:37.66 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:38:37.67 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:38:37.71 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:38:37.71 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:38:37.71 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:38:37.75 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:38:37.75 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:38:37.77 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:38:37.79 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:38:37.80 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:38:37.82 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:38:37.88 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:38:37.96 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/residuals_linear.rds
2026-03-03 20:38:38.00 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/fitted_linear.rds
2026-03-03 20:38:38.04 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/residuals_logistic.rds
2026-03-03 20:38:38.24 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/fitted_logistic.rds
2026-03-03 20:38:48.84 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:38:48.87 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:38:48.93 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:38:48.94 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:38:48.95 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:38:48.98 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:38:48.99 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:38:48.99 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:38:49.02 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:38:49.03 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:38:49.05 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:38:49.06 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:38:49.07 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:38:49.09 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:38:49.12 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:38:54.41 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:38:54.46 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:38:54.49 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:38:54.50 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:38:54.51 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:38:54.54 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:38:54.54 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:38:54.54 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:38:54.58 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:38:54.59 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:38:54.61 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:38:54.62 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:38:54.63 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:38:54.64 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:38:54.67 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:38:54.75 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/residuals_linear.rds
2026-03-03 20:38:54.79 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/fitted_linear.rds
2026-03-03 20:38:54.83 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/residuals_logistic.rds
2026-03-03 20:38:55.02 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/fitted_logistic.rds
2026-03-03 20:39:04.49 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:39:04.51 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:39:04.55 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:39:04.56 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:39:04.57 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:39:04.61 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:39:04.61 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:39:04.62 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:39:04.65 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:39:04.66 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:39:04.67 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:39:04.69 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:39:04.70 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:39:04.71 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:39:04.74 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:39:11.08 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:39:11.11 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:39:11.16 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:39:11.17 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:39:11.19 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:39:11.21 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:39:11.21 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:39:11.22 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:39:11.25 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:39:11.25 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:39:11.27 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:39:11.28 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:39:11.29 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:39:11.30 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:39:11.33 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:39:11.40 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/residuals_linear.rds
2026-03-03 20:39:11.43 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/fitted_linear.rds
2026-03-03 20:39:11.47 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/residuals_logistic.rds
2026-03-03 20:39:11.66 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5321cf7e37e/fits/fitted_logistic.rds
2026-03-03 20:39:20.41 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:39:20.44 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:39:20.47 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:39:20.48 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:39:20.51 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:39:20.54 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:39:20.54 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:39:20.54 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:39:20.58 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:39:20.58 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:39:20.60 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:39:20.62 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:39:20.62 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:39:20.64 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:39:20.66 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:39:25.88 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:39:25.91 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:39:25.94 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:39:25.95 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:39:25.96 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:39:25.99 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:39:25.99 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:39:26.00 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:39:26.04 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:39:26.04 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:39:26.07 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:39:26.08 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:39:26.09 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:39:26.10 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:39:26.14 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:39:36.54 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:39:40.49 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:39:50.75 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:39:54.98 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:39:55.22 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_linear.rds
2026-03-03 20:39:55.25 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_linear.rds
2026-03-03 20:39:55.27 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_logistic.rds
2026-03-03 20:39:55.32 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_logistic.rds
2026-03-03 20:40:05.30 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:40:07.52 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:40:07.64 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_linear.rds
2026-03-03 20:40:07.68 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_linear.rds
2026-03-03 20:40:07.71 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_logistic.rds
2026-03-03 20:40:07.75 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_logistic.rds
2026-03-03 20:40:16.01 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:40:18.96 WARNING::Fitting problem for feature 124 returning NA
2026-03-03 20:40:19.07 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_linear.rds
2026-03-03 20:40:19.10 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_linear.rds
2026-03-03 20:40:19.12 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_logistic.rds
2026-03-03 20:40:19.17 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_logistic.rds
2026-03-03 20:40:27.19 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:40:27.21 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:40:27.24 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:40:27.25 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:40:27.26 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:40:27.29 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:40:27.29 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:40:27.30 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:40:27.34 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:40:27.34 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:40:27.36 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:40:27.39 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:40:27.40 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:40:27.42 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:40:27.44 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:40:33.39 WARNING::Fitting problem for feature 50 returning NA
2026-03-03 20:40:33.41 WARNING::Fitting problem for feature 62 returning NA
2026-03-03 20:40:33.44 WARNING::Fitting problem for feature 74 returning NA
2026-03-03 20:40:33.45 WARNING::Fitting problem for feature 78 returning NA
2026-03-03 20:40:33.46 WARNING::Fitting problem for feature 84 returning NA
2026-03-03 20:40:33.50 WARNING::Fitting problem for feature 96 returning NA
2026-03-03 20:40:33.50 WARNING::Fitting problem for feature 97 returning NA
2026-03-03 20:40:33.51 WARNING::Fitting problem for feature 99 returning NA
2026-03-03 20:40:33.55 WARNING::Fitting problem for feature 114 returning NA
2026-03-03 20:40:33.55 WARNING::Fitting problem for feature 115 returning NA
2026-03-03 20:40:33.57 WARNING::Fitting problem for feature 123 returning NA
2026-03-03 20:40:33.59 WARNING::Fitting problem for feature 130 returning NA
2026-03-03 20:40:33.60 WARNING::Fitting problem for feature 132 returning NA
2026-03-03 20:40:33.62 WARNING::Fitting problem for feature 139 returning NA
2026-03-03 20:40:33.65 WARNING::Fitting problem for feature 150 returning NA
2026-03-03 20:40:33.77 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_linear.rds
2026-03-03 20:40:33.81 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_linear.rds
2026-03-03 20:40:33.84 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/residuals_logistic.rds
2026-03-03 20:40:34.02 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed532582ab6fc/fits/fitted_logistic.rds
2026-03-03 20:40:42.81 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-03 20:40:42.82 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-03 20:40:42.83 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-03 20:40:42.85 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-03 20:40:42.86 ERROR::Effect name not found in metadata: d
2026-03-03 20:40:42.86 ERROR::No user formula provided
2026-03-03 20:40:42.87 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-03 20:40:42.89 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-03 20:40:44.06 INFO::Writing function arguments to log file
2026-03-03 20:40:44.07 INFO::Verifying options selected are valid
2026-03-03 20:40:45.02 INFO::Writing function arguments to log file
2026-03-03 20:40:45.03 INFO::Verifying options selected are valid
2026-03-03 20:40:45.03 INFO::Determining format of input files
2026-03-03 20:40:45.03 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-03 20:40:45.03 INFO::Running selected normalization method: TSS
2026-03-03 20:40:45.03 INFO::Creating output feature tables folder
2026-03-03 20:40:45.03 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/features/data_norm.tsv
2026-03-03 20:40:45.03 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-03 20:40:45.03 INFO::Total samples in data: 16
2026-03-03 20:40:45.03 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-03 20:40:45.03 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-03 20:40:45.03 INFO::Total filtered features: 0
2026-03-03 20:40:45.03 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-03 20:40:45.03 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-03 20:40:45.03 INFO::Filtered feature names from variance filtering:
2026-03-03 20:40:45.04 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/features/filtered_data.tsv
2026-03-03 20:40:45.04 INFO::Running selected transform method: LOG
2026-03-03 20:40:45.04 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/features/data_transformed.tsv
2026-03-03 20:40:45.04 INFO::Applying z-score to standardize continuous metadata
2026-03-03 20:40:45.04 INFO::Running the linear model component
2026-03-03 20:40:45.05 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:45.05 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:45.05 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:45.05 INFO::Counting total values for each feature
2026-03-03 20:40:45.05 INFO::Running the logistic model component
2026-03-03 20:40:45.06 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:45.06 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:45.07 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:45.07 INFO::Counting total values for each feature
2026-03-03 20:40:45.07 INFO::Re-running abundances for warn_prevalence
2026-03-03 20:40:45.07 INFO::Running selected normalization method: TSS
2026-03-03 20:40:45.07 INFO::Running selected transform method: LOG
2026-03-03 20:40:45.08 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:45.08 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:45.08 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:45.11 INFO::Creating fits folder
2026-03-03 20:40:45.11 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/fits/residuals_linear.rds
2026-03-03 20:40:45.11 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/fits/fitted_linear.rds
2026-03-03 20:40:45.11 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/fits/residuals_logistic.rds
2026-03-03 20:40:45.11 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/fits/fitted_logistic.rds
2026-03-03 20:40:45.11 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/all_results.tsv
2026-03-03 20:40:45.11 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//RtmpN5xA2M/filed5327fde5c8a/significant_results.tsv
2026-03-03 20:40:45.11 INFO::Creating output figures folder
2026-03-03 20:40:45.11 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/figures/summary_plot.pdf
2026-03-03 20:40:45.81 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/figures
2026-03-03 20:40:45.81 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-03 20:40:45.81 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-03 20:40:46.07 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/figures/summary_plot.pdf
2026-03-03 20:40:46.73 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5327fde5c8a/figures
2026-03-03 20:40:46.73 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-03 20:40:46.74 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-03 20:40:46.96 INFO::Running the linear model component
2026-03-03 20:40:46.96 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:46.96 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:46.97 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:46.97 INFO::Counting total values for each feature
2026-03-03 20:40:46.97 INFO::Running the logistic model component
2026-03-03 20:40:46.97 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:46.97 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:46.98 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:46.98 INFO::Counting total values for each feature
2026-03-03 20:40:46.98 INFO::Re-running abundances for warn_prevalence
2026-03-03 20:40:46.98 INFO::Running selected normalization method: TSS
2026-03-03 20:40:46.98 INFO::Running selected transform method: LOG
2026-03-03 20:40:46.99 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:46.99 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:46.99 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:47.03 INFO::Creating output folder
2026-03-03 20:40:47.03 INFO::Creating output figures folder
2026-03-03 20:40:47.03 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed53210ed6af6/figures/summary_plot.pdf
2026-03-03 20:40:47.67 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed53210ed6af6/figures
2026-03-03 20:40:47.67 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-03 20:40:47.67 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-03 20:40:48.10 INFO::Applying z-score to standardize continuous metadata
2026-03-03 20:40:48.10 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-03 20:40:48.10 INFO::Bypass z-score application to metadata
2026-03-03 20:40:48.10 INFO::Bypass z-score application to metadata
2026-03-03 20:40:48.12 INFO::Determining format of input files
2026-03-03 20:40:48.12 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-03 20:40:48.12 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-03 20:40:48.12 INFO::Determining format of input files
2026-03-03 20:40:48.13 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-03 20:40:48.13 INFO::Input format is feature_specific_covariate samples as columns
2026-03-03 20:40:48.13 INFO::Determining format of input files
2026-03-03 20:40:48.13 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-03 20:40:48.13 INFO::Input format is feature_specific_covariate samples as columns
2026-03-03 20:40:48.13 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-03 20:40:48.13 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-03 20:40:48.13 INFO::Running selected transform method: LOG
2026-03-03 20:40:48.13 INFO::Creating output feature tables folder
2026-03-03 20:40:48.14 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5322a20dee6/features/data_transformed.tsv
2026-03-03 20:40:48.14 INFO::Running selected transform method: LOG
2026-03-03 20:40:48.14 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5322a20dee6/features/data_transformed.tsv
2026-03-03 20:40:48.14 INFO::Running selected transform method: PLOG
2026-03-03 20:40:48.14 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5322a20dee6/features/data_transformed.tsv
2026-03-03 20:40:48.14 INFO::Running selected transform method: NONE
2026-03-03 20:40:48.14 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5322a20dee6/features/data_transformed.tsv
2026-03-03 20:40:48.14 INFO::Running the linear model component
2026-03-03 20:40:48.15 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:48.15 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:48.15 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:48.15 INFO::Counting total values for each feature
2026-03-03 20:40:48.15 INFO::Running the logistic model component
2026-03-03 20:40:48.16 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:48.16 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:48.16 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:48.16 INFO::Counting total values for each feature
2026-03-03 20:40:48.16 INFO::Re-running abundances for warn_prevalence
2026-03-03 20:40:48.16 INFO::Running selected normalization method: TSS
2026-03-03 20:40:48.16 INFO::Running selected transform method: LOG
2026-03-03 20:40:48.17 INFO::Fitting model to feature number 1, a
2026-03-03 20:40:48.17 INFO::Fitting model to feature number 2, b
2026-03-03 20:40:48.17 INFO::Fitting model to feature number 3, c
2026-03-03 20:40:48.20 INFO::Creating output folder
2026-03-03 20:40:48.20 INFO::Creating fits folder
2026-03-03 20:40:48.21 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5325409e3a5/fits/residuals_linear.rds
2026-03-03 20:40:48.21 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5325409e3a5/fits/fitted_linear.rds
2026-03-03 20:40:48.21 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5325409e3a5/fits/residuals_logistic.rds
2026-03-03 20:40:48.21 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5325409e3a5/fits/fitted_logistic.rds
2026-03-03 20:40:48.21 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpN5xA2M/filed5325409e3a5/all_results.tsv
2026-03-03 20:40:48.21 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//RtmpN5xA2M/filed5325409e3a5/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
143.788 4.408 156.939
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 7.065 | 0.468 | 7.740 | |
| maaslin_check_arguments | 0.062 | 0.002 | 0.068 | |
| maaslin_check_formula | 0.064 | 0.004 | 0.089 | |
| maaslin_compute_formula | 0.071 | 0.004 | 0.076 | |
| maaslin_contrast_test | 6.843 | 0.616 | 8.028 | |
| maaslin_filter | 0.239 | 0.022 | 0.290 | |
| maaslin_fit | 5.073 | 0.580 | 5.980 | |
| maaslin_log_arguments | 0.061 | 0.004 | 0.065 | |
| maaslin_normalize | 0.135 | 0.011 | 0.154 | |
| maaslin_plot_results | 17.241 | 0.883 | 19.129 | |
| maaslin_plot_results_from_output | 17.217 | 0.703 | 18.865 | |
| maaslin_process_metadata | 0.241 | 0.020 | 0.271 | |
| maaslin_read_data | 0.074 | 0.004 | 0.087 | |
| maaslin_reorder_data | 0.065 | 0.003 | 0.070 | |
| maaslin_transform | 0.299 | 0.025 | 0.342 | |
| maaslin_write_results | 5.736 | 0.626 | 6.747 | |
| maaslin_write_results_lefse_format | 6.016 | 0.653 | 6.984 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.002 | |