William Nickols
| Snapshot Date: 2026-03-04 13:40 -0500 (Wed, 04 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 2026-03-05 11:35 -0500 (Thu, 05 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" | 4891 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4583 |
| 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: 2026-03-04 20:36:56 -0500 (Wed, 04 Mar 2026) |
| EndedAt: 2026-03-04 20:41:21 -0500 (Wed, 04 Mar 2026) |
| EllapsedTime: 264.6 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 17.494 0.898 19.584
maaslin_plot_results_from_output 17.203 0.828 18.852
maaslin3 7.388 0.557 8.275
maaslin_contrast_test 6.906 0.623 8.042
maaslin_write_results_lefse_format 6.087 0.582 6.921
maaslin_write_results 5.755 0.540 6.653
maaslin_fit 5.084 0.580 6.044
* 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")
2026-03-04 20:38:40.59 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:38:40.62 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:38:40.66 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:38:40.67 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:38:40.68 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:38:40.72 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:38:40.72 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:38:40.73 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:38:40.77 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:38:40.78 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:38:40.80 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:38:40.82 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:38:40.82 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:38:40.84 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:38:40.87 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:38:46.80 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:38:46.83 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:38:46.88 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:38:46.89 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:38:46.91 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:38:46.93 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:38:46.94 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:38:46.94 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:38:46.98 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:38:46.98 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:38:47.00 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:38:47.02 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:38:47.02 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:38:47.04 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:38:47.06 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:38:48.905 R[12409:91463535] XType: Using static font registry.
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-04 20:38:59.94 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:38:59.97 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:00.00 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:00.01 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:00.03 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:00.06 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:00.06 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:00.07 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:00.10 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:00.11 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:00.13 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:00.14 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:00.15 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:00.17 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:00.20 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:05.49 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:05.51 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:05.54 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:05.55 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:05.57 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:05.60 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:05.60 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:05.61 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:05.64 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:05.64 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:05.66 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:05.69 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:05.69 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:05.71 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:05.75 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:05.84 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/residuals_linear.rds
2026-03-04 20:39:05.87 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/fitted_linear.rds
2026-03-04 20:39:05.91 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/residuals_logistic.rds
2026-03-04 20:39:06.09 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/fitted_logistic.rds
2026-03-04 20:39:16.76 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:16.79 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:16.85 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:16.86 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:16.88 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:16.91 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:16.91 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:16.91 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:16.95 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:16.95 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:16.97 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:16.99 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:16.99 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:17.02 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:17.05 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:22.36 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:22.39 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:22.42 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:22.43 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:22.45 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:22.47 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:22.48 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:22.48 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:22.52 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:22.52 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:22.54 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:22.56 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:22.57 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:22.59 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:22.63 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:22.71 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/residuals_linear.rds
2026-03-04 20:39:22.75 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/fitted_linear.rds
2026-03-04 20:39:22.79 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/residuals_logistic.rds
2026-03-04 20:39:23.00 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/fitted_logistic.rds
2026-03-04 20:39:33.63 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:33.66 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:33.69 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:33.70 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:33.72 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:33.75 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:33.75 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:33.76 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:33.80 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:33.80 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:33.82 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:33.84 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:33.84 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:33.87 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:33.90 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:39.29 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:39.33 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:39.36 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:39.36 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:39.38 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:39.41 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:39.41 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:39.41 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:39.45 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:39.45 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:39.47 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:39.49 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:39.49 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:39.51 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:39.54 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:39.66 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/residuals_linear.rds
2026-03-04 20:39:39.70 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/fitted_linear.rds
2026-03-04 20:39:39.74 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/residuals_logistic.rds
2026-03-04 20:39:39.95 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079452312e0/fits/fitted_logistic.rds
2026-03-04 20:39:48.86 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:48.88 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:48.91 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:48.92 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:48.93 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:48.96 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:48.96 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:48.97 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:49.00 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:49.01 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:49.03 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:49.05 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:49.05 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:49.06 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:49.09 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:39:54.26 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:39:54.29 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:39:54.32 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:39:54.33 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:39:54.34 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:39:54.38 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:39:54.38 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:39:54.38 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:39:54.42 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:39:54.43 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:39:54.45 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:39:54.46 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:39:54.47 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:39:54.49 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:39:54.52 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:40:04.17 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:08.18 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:18.93 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:22.45 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:22.67 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_linear.rds
2026-03-04 20:40:22.70 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_linear.rds
2026-03-04 20:40:22.73 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_logistic.rds
2026-03-04 20:40:22.78 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_logistic.rds
2026-03-04 20:40:32.85 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:35.69 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:35.81 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_linear.rds
2026-03-04 20:40:35.84 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_linear.rds
2026-03-04 20:40:35.87 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_logistic.rds
2026-03-04 20:40:35.92 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_logistic.rds
2026-03-04 20:40:44.09 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:46.93 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 20:40:47.03 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_linear.rds
2026-03-04 20:40:47.07 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_linear.rds
2026-03-04 20:40:47.10 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_logistic.rds
2026-03-04 20:40:47.14 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_logistic.rds
2026-03-04 20:40:55.17 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:40:55.84 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:40:55.86 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:40:55.87 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:40:55.88 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:40:55.91 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:40:55.92 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:40:55.92 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:40:55.96 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:40:55.96 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:40:55.99 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:40:56.01 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:40:56.01 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:40:56.03 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:40:56.05 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:41:00.89 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 20:41:00.93 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 20:41:00.97 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 20:41:00.98 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 20:41:01.00 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 20:41:01.03 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 20:41:01.03 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 20:41:01.04 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 20:41:01.07 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 20:41:01.07 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 20:41:01.09 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 20:41:01.11 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 20:41:01.12 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 20:41:01.14 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 20:41:01.16 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 20:41:01.29 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_linear.rds
2026-03-04 20:41:01.33 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_linear.rds
2026-03-04 20:41:01.37 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/residuals_logistic.rds
2026-03-04 20:41:01.57 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30796bb0d268/fits/fitted_logistic.rds
2026-03-04 20:41:10.94 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-04 20:41:10.95 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-04 20:41:10.95 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-04 20:41:10.97 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-04 20:41:10.98 ERROR::Effect name not found in metadata: d
2026-03-04 20:41:10.98 ERROR::No user formula provided
2026-03-04 20:41:10.99 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-04 20:41:11.00 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-04 20:41:12.15 INFO::Writing function arguments to log file
2026-03-04 20:41:12.15 INFO::Verifying options selected are valid
2026-03-04 20:41:13.08 INFO::Writing function arguments to log file
2026-03-04 20:41:13.09 INFO::Verifying options selected are valid
2026-03-04 20:41:13.09 INFO::Determining format of input files
2026-03-04 20:41:13.09 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 20:41:13.09 INFO::Running selected normalization method: TSS
2026-03-04 20:41:13.09 INFO::Creating output feature tables folder
2026-03-04 20:41:13.09 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/features/data_norm.tsv
2026-03-04 20:41:13.09 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-04 20:41:13.09 INFO::Total samples in data: 16
2026-03-04 20:41:13.09 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-04 20:41:13.09 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-04 20:41:13.09 INFO::Total filtered features: 0
2026-03-04 20:41:13.09 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-04 20:41:13.10 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-04 20:41:13.10 INFO::Filtered feature names from variance filtering:
2026-03-04 20:41:13.10 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/features/filtered_data.tsv
2026-03-04 20:41:13.10 INFO::Running selected transform method: LOG
2026-03-04 20:41:13.10 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/features/data_transformed.tsv
2026-03-04 20:41:13.10 INFO::Applying z-score to standardize continuous metadata
2026-03-04 20:41:13.10 INFO::Running the linear model component
2026-03-04 20:41:13.11 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:13.11 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:13.11 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:13.11 INFO::Counting total values for each feature
2026-03-04 20:41:13.11 INFO::Running the logistic model component
2026-03-04 20:41:13.12 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:13.12 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:13.13 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:13.13 INFO::Counting total values for each feature
2026-03-04 20:41:13.13 INFO::Re-running abundances for warn_prevalence
2026-03-04 20:41:13.13 INFO::Running selected normalization method: TSS
2026-03-04 20:41:13.13 INFO::Running selected transform method: LOG
2026-03-04 20:41:13.14 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:13.14 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:13.14 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:13.17 INFO::Creating fits folder
2026-03-04 20:41:13.17 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/fits/residuals_linear.rds
2026-03-04 20:41:13.17 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/fits/fitted_linear.rds
2026-03-04 20:41:13.17 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/fits/residuals_logistic.rds
2026-03-04 20:41:13.17 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/fits/fitted_logistic.rds
2026-03-04 20:41:13.17 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/all_results.tsv
2026-03-04 20:41:13.17 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//RtmpXWLhBZ/file307917c79009/significant_results.tsv
2026-03-04 20:41:13.17 INFO::Creating output figures folder
2026-03-04 20:41:13.17 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/figures/summary_plot.pdf
2026-03-04 20:41:13.88 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/figures
2026-03-04 20:41:13.89 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-04 20:41:13.89 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-04 20:41:14.10 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/figures/summary_plot.pdf
2026-03-04 20:41:14.77 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file307917c79009/figures
2026-03-04 20:41:14.78 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-04 20:41:14.78 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-04 20:41:15.01 INFO::Running the linear model component
2026-03-04 20:41:15.01 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:15.02 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:15.02 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:15.02 INFO::Counting total values for each feature
2026-03-04 20:41:15.02 INFO::Running the logistic model component
2026-03-04 20:41:15.02 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:15.03 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:15.03 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:15.03 INFO::Counting total values for each feature
2026-03-04 20:41:15.03 INFO::Re-running abundances for warn_prevalence
2026-03-04 20:41:15.03 INFO::Running selected normalization method: TSS
2026-03-04 20:41:15.03 INFO::Running selected transform method: LOG
2026-03-04 20:41:15.04 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:15.04 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:15.04 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:15.06 INFO::Creating output folder
2026-03-04 20:41:15.06 INFO::Creating output figures folder
2026-03-04 20:41:15.07 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792555ef14/figures/summary_plot.pdf
2026-03-04 20:41:15.73 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792555ef14/figures
2026-03-04 20:41:15.73 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-04 20:41:15.73 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-04 20:41:16.16 INFO::Applying z-score to standardize continuous metadata
2026-03-04 20:41:16.17 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-04 20:41:16.17 INFO::Bypass z-score application to metadata
2026-03-04 20:41:16.17 INFO::Bypass z-score application to metadata
2026-03-04 20:41:16.19 INFO::Determining format of input files
2026-03-04 20:41:16.19 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 20:41:16.19 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-04 20:41:16.19 INFO::Determining format of input files
2026-03-04 20:41:16.20 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-04 20:41:16.20 INFO::Input format is feature_specific_covariate samples as columns
2026-03-04 20:41:16.20 INFO::Determining format of input files
2026-03-04 20:41:16.20 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 20:41:16.20 INFO::Input format is feature_specific_covariate samples as columns
2026-03-04 20:41:16.20 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-04 20:41:16.20 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-04 20:41:16.20 INFO::Running selected transform method: LOG
2026-03-04 20:41:16.20 INFO::Creating output feature tables folder
2026-03-04 20:41:16.21 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079a42db97/features/data_transformed.tsv
2026-03-04 20:41:16.21 INFO::Running selected transform method: LOG
2026-03-04 20:41:16.21 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079a42db97/features/data_transformed.tsv
2026-03-04 20:41:16.21 INFO::Running selected transform method: PLOG
2026-03-04 20:41:16.21 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079a42db97/features/data_transformed.tsv
2026-03-04 20:41:16.21 INFO::Running selected transform method: NONE
2026-03-04 20:41:16.21 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file3079a42db97/features/data_transformed.tsv
2026-03-04 20:41:16.21 INFO::Running the linear model component
2026-03-04 20:41:16.22 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:16.22 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:16.22 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:16.22 INFO::Counting total values for each feature
2026-03-04 20:41:16.22 INFO::Running the logistic model component
2026-03-04 20:41:16.23 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:16.23 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:16.23 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:16.23 INFO::Counting total values for each feature
2026-03-04 20:41:16.23 INFO::Re-running abundances for warn_prevalence
2026-03-04 20:41:16.23 INFO::Running selected normalization method: TSS
2026-03-04 20:41:16.23 INFO::Running selected transform method: LOG
2026-03-04 20:41:16.24 INFO::Fitting model to feature number 1, a
2026-03-04 20:41:16.24 INFO::Fitting model to feature number 2, b
2026-03-04 20:41:16.24 INFO::Fitting model to feature number 3, c
2026-03-04 20:41:16.26 INFO::Creating output folder
2026-03-04 20:41:16.26 INFO::Creating fits folder
2026-03-04 20:41:16.26 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792b5e9bc4/fits/residuals_linear.rds
2026-03-04 20:41:16.27 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792b5e9bc4/fits/fitted_linear.rds
2026-03-04 20:41:16.27 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792b5e9bc4/fits/residuals_logistic.rds
2026-03-04 20:41:16.27 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792b5e9bc4/fits/fitted_logistic.rds
2026-03-04 20:41:16.27 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXWLhBZ/file30792b5e9bc4/all_results.tsv
2026-03-04 20:41:16.27 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//RtmpXWLhBZ/file30792b5e9bc4/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
143.198 4.465 157.159
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 7.388 | 0.557 | 8.275 | |
| maaslin_check_arguments | 0.054 | 0.001 | 0.060 | |
| maaslin_check_formula | 0.057 | 0.003 | 0.067 | |
| maaslin_compute_formula | 0.067 | 0.005 | 0.083 | |
| maaslin_contrast_test | 6.906 | 0.623 | 8.042 | |
| maaslin_filter | 0.241 | 0.031 | 0.303 | |
| maaslin_fit | 5.084 | 0.580 | 6.044 | |
| maaslin_log_arguments | 0.062 | 0.004 | 0.079 | |
| maaslin_normalize | 0.148 | 0.018 | 0.193 | |
| maaslin_plot_results | 17.494 | 0.898 | 19.584 | |
| maaslin_plot_results_from_output | 17.203 | 0.828 | 18.852 | |
| maaslin_process_metadata | 0.236 | 0.022 | 0.261 | |
| maaslin_read_data | 0.058 | 0.004 | 0.061 | |
| maaslin_reorder_data | 0.058 | 0.003 | 0.064 | |
| maaslin_transform | 0.300 | 0.029 | 0.347 | |
| maaslin_write_results | 5.755 | 0.540 | 6.653 | |
| maaslin_write_results_lefse_format | 6.087 | 0.582 | 6.921 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.001 | 0.002 | |