William Nickols
| Snapshot Date: 2026-03-12 13:40 -0400 (Thu, 12 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 2026-03-13 11:34 -0400 (Fri, 13 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" | 4819 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 1172/2360 | 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: 2026-03-12 19:11:14 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 19:15:37 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 262.5 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: 2026-03-12 23:11:14 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 17.651 0.732 19.139
maaslin_plot_results 17.481 0.847 19.161
maaslin_contrast_test 6.914 0.612 7.709
maaslin3 6.997 0.471 7.719
maaslin_write_results_lefse_format 5.937 0.489 6.751
maaslin_write_results 5.794 0.553 6.564
maaslin_fit 5.035 0.553 5.790
* 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")
2026-03-12 19:12:56.27 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:12:56.30 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:12:56.36 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:12:56.37 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:12:56.39 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:12:56.42 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:12:56.43 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:12:56.43 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:12:56.47 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:12:56.47 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:12:56.50 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:12:56.52 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:12:56.52 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:12:56.54 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:12:56.57 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:02.51 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:02.54 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:02.57 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:02.58 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:02.59 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:02.62 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:02.63 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:02.63 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:02.67 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:02.67 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:02.69 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:02.70 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:02.71 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:02.73 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:02.75 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:04.466 R[4948:143152613] XType: Using static font registry.
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-12 19:13:14.90 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:14.94 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:14.97 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:14.98 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:15.45 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:15.48 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:15.48 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:15.49 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:15.53 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:15.53 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:15.55 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:15.56 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:15.57 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:15.58 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:15.61 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:21.06 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:21.09 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:21.12 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:21.13 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:21.14 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:21.18 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:21.18 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:21.19 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:21.23 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:21.23 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:21.25 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:21.27 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:21.27 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:21.29 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:21.33 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:21.40 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/residuals_linear.rds
2026-03-12 19:13:21.44 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/fitted_linear.rds
2026-03-12 19:13:21.48 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/residuals_logistic.rds
2026-03-12 19:13:21.67 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/fitted_logistic.rds
2026-03-12 19:13:31.16 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:31.19 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:31.22 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:31.23 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:31.24 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:31.27 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:31.27 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:31.28 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:31.31 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:31.32 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:31.33 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:31.35 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:31.35 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:31.37 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:31.41 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:37.51 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:37.54 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:37.59 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:37.60 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:37.61 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:37.64 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:37.64 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:37.65 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:37.68 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:37.68 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:37.70 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:37.71 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:37.72 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:37.73 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:37.76 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:37.84 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/residuals_linear.rds
2026-03-12 19:13:37.88 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/fitted_linear.rds
2026-03-12 19:13:37.92 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/residuals_logistic.rds
2026-03-12 19:13:38.10 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/fitted_logistic.rds
2026-03-12 19:13:47.05 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:47.08 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:47.12 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:47.13 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:47.14 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:47.18 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:47.18 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:47.18 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:47.23 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:47.25 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:47.27 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:47.29 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:47.29 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:47.31 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:47.34 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:52.53 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:13:52.56 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:13:52.59 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:13:52.60 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:13:52.61 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:13:52.64 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:13:52.65 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:13:52.65 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:13:52.69 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:13:52.70 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:13:52.74 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:13:52.76 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:13:52.77 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:13:52.78 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:13:52.81 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:13:52.89 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/residuals_linear.rds
2026-03-12 19:13:52.93 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/fitted_linear.rds
2026-03-12 19:13:52.97 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/residuals_logistic.rds
2026-03-12 19:13:53.16 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135430242db/fits/fitted_logistic.rds
2026-03-12 19:14:02.48 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:14:02.51 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:14:02.54 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:14:02.55 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:14:02.56 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:14:02.60 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:14:02.60 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:14:02.60 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:14:02.64 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:14:02.64 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:14:02.66 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:14:02.67 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:14:02.68 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:14:02.70 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:14:02.72 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:14:07.31 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:14:07.34 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:14:07.37 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:14:07.38 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:14:07.40 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:14:07.43 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:14:07.43 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:14:07.43 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:14:07.48 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:14:07.48 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:14:07.53 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:14:07.54 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:14:07.55 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:14:07.57 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:14:07.60 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:14:17.84 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:14:22.46 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:14:33.17 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:14:36.76 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:14:36.98 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_linear.rds
2026-03-12 19:14:37.01 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_linear.rds
2026-03-12 19:14:37.04 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_logistic.rds
2026-03-12 19:14:37.08 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_logistic.rds
2026-03-12 19:14:47.35 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:14:49.54 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:14:49.65 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_linear.rds
2026-03-12 19:14:49.70 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_linear.rds
2026-03-12 19:14:49.72 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_logistic.rds
2026-03-12 19:14:49.76 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_logistic.rds
2026-03-12 19:14:58.47 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:15:01.31 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 19:15:01.43 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_linear.rds
2026-03-12 19:15:01.47 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_linear.rds
2026-03-12 19:15:01.50 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_logistic.rds
2026-03-12 19:15:01.55 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_logistic.rds
2026-03-12 19:15:09.75 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:15:09.78 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:15:09.81 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:15:09.82 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:15:09.85 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:15:09.88 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:15:09.88 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:15:09.89 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:15:09.92 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:15:09.92 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:15:09.94 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:15:09.96 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:15:09.96 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:15:09.98 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:15:10.00 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:15:15.33 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 19:15:15.37 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 19:15:15.45 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 19:15:15.45 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 19:15:15.47 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 19:15:15.50 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 19:15:15.50 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 19:15:15.51 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 19:15:15.55 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 19:15:15.56 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 19:15:15.58 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 19:15:15.60 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 19:15:15.61 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 19:15:15.62 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 19:15:15.67 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 19:15:15.76 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_linear.rds
2026-03-12 19:15:15.85 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_linear.rds
2026-03-12 19:15:15.90 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/residuals_logistic.rds
2026-03-12 19:15:16.15 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13543b691f5c/fits/fitted_logistic.rds
2026-03-12 19:15:26.11 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-12 19:15:26.11 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-12 19:15:26.12 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-12 19:15:26.14 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-12 19:15:26.15 ERROR::Effect name not found in metadata: d
2026-03-12 19:15:26.15 ERROR::No user formula provided
2026-03-12 19:15:26.16 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-12 19:15:26.17 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-12 19:15:27.36 INFO::Writing function arguments to log file
2026-03-12 19:15:27.37 INFO::Verifying options selected are valid
2026-03-12 19:15:28.31 INFO::Writing function arguments to log file
2026-03-12 19:15:28.32 INFO::Verifying options selected are valid
2026-03-12 19:15:28.32 INFO::Determining format of input files
2026-03-12 19:15:28.32 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-12 19:15:28.32 INFO::Running selected normalization method: TSS
2026-03-12 19:15:28.32 INFO::Creating output feature tables folder
2026-03-12 19:15:28.32 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/features/data_norm.tsv
2026-03-12 19:15:28.32 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-12 19:15:28.32 INFO::Total samples in data: 16
2026-03-12 19:15:28.32 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-12 19:15:28.32 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-12 19:15:28.32 INFO::Total filtered features: 0
2026-03-12 19:15:28.33 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-12 19:15:28.33 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-12 19:15:28.33 INFO::Filtered feature names from variance filtering:
2026-03-12 19:15:28.33 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/features/filtered_data.tsv
2026-03-12 19:15:28.33 INFO::Running selected transform method: LOG
2026-03-12 19:15:28.33 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/features/data_transformed.tsv
2026-03-12 19:15:28.33 INFO::Applying z-score to standardize continuous metadata
2026-03-12 19:15:28.33 INFO::Running the linear model component
2026-03-12 19:15:28.35 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:28.35 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:28.35 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:28.35 INFO::Counting total values for each feature
2026-03-12 19:15:28.35 INFO::Running the logistic model component
2026-03-12 19:15:28.36 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:28.36 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:28.37 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:28.37 INFO::Counting total values for each feature
2026-03-12 19:15:28.37 INFO::Re-running abundances for warn_prevalence
2026-03-12 19:15:28.37 INFO::Running selected normalization method: TSS
2026-03-12 19:15:28.37 INFO::Running selected transform method: LOG
2026-03-12 19:15:28.38 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:28.38 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:28.38 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:28.41 INFO::Creating fits folder
2026-03-12 19:15:28.41 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/fits/residuals_linear.rds
2026-03-12 19:15:28.41 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/fits/fitted_linear.rds
2026-03-12 19:15:28.41 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/fits/residuals_logistic.rds
2026-03-12 19:15:28.41 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/fits/fitted_logistic.rds
2026-03-12 19:15:28.41 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/all_results.tsv
2026-03-12 19:15:28.42 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//RtmplTRxDr/file13542df499a7/significant_results.tsv
2026-03-12 19:15:28.42 INFO::Creating output figures folder
2026-03-12 19:15:28.42 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/figures/summary_plot.pdf
2026-03-12 19:15:29.10 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/figures
2026-03-12 19:15:29.10 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-12 19:15:29.10 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-12 19:15:29.32 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/figures/summary_plot.pdf
2026-03-12 19:15:30.01 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13542df499a7/figures
2026-03-12 19:15:30.01 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-12 19:15:30.01 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-12 19:15:30.24 INFO::Running the linear model component
2026-03-12 19:15:30.25 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:30.25 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:30.25 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:30.25 INFO::Counting total values for each feature
2026-03-12 19:15:30.25 INFO::Running the logistic model component
2026-03-12 19:15:30.25 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:30.26 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:30.26 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:30.26 INFO::Counting total values for each feature
2026-03-12 19:15:30.26 INFO::Re-running abundances for warn_prevalence
2026-03-12 19:15:30.26 INFO::Running selected normalization method: TSS
2026-03-12 19:15:30.26 INFO::Running selected transform method: LOG
2026-03-12 19:15:30.26 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:30.27 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:30.27 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:30.29 INFO::Creating output folder
2026-03-12 19:15:30.29 INFO::Creating output figures folder
2026-03-12 19:15:30.30 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135464acd78e/figures/summary_plot.pdf
2026-03-12 19:15:31.13 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file135464acd78e/figures
2026-03-12 19:15:31.13 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-12 19:15:31.13 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-12 19:15:31.60 INFO::Applying z-score to standardize continuous metadata
2026-03-12 19:15:31.60 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-12 19:15:31.60 INFO::Bypass z-score application to metadata
2026-03-12 19:15:31.61 INFO::Bypass z-score application to metadata
2026-03-12 19:15:31.63 INFO::Determining format of input files
2026-03-12 19:15:31.63 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-12 19:15:31.63 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-12 19:15:31.63 INFO::Determining format of input files
2026-03-12 19:15:31.63 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-12 19:15:31.63 INFO::Input format is feature_specific_covariate samples as columns
2026-03-12 19:15:31.64 INFO::Determining format of input files
2026-03-12 19:15:31.64 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-12 19:15:31.65 INFO::Input format is feature_specific_covariate samples as columns
2026-03-12 19:15:31.65 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-12 19:15:31.65 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-12 19:15:31.65 INFO::Running selected transform method: LOG
2026-03-12 19:15:31.65 INFO::Creating output feature tables folder
2026-03-12 19:15:31.65 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13545dace51f/features/data_transformed.tsv
2026-03-12 19:15:31.66 INFO::Running selected transform method: LOG
2026-03-12 19:15:31.66 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13545dace51f/features/data_transformed.tsv
2026-03-12 19:15:31.66 INFO::Running selected transform method: PLOG
2026-03-12 19:15:31.66 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13545dace51f/features/data_transformed.tsv
2026-03-12 19:15:31.67 INFO::Running selected transform method: NONE
2026-03-12 19:15:31.67 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13545dace51f/features/data_transformed.tsv
2026-03-12 19:15:31.67 INFO::Running the linear model component
2026-03-12 19:15:31.68 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:31.68 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:31.69 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:31.69 INFO::Counting total values for each feature
2026-03-12 19:15:31.69 INFO::Running the logistic model component
2026-03-12 19:15:31.69 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:31.70 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:31.70 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:31.70 INFO::Counting total values for each feature
2026-03-12 19:15:31.70 INFO::Re-running abundances for warn_prevalence
2026-03-12 19:15:31.70 INFO::Running selected normalization method: TSS
2026-03-12 19:15:31.70 INFO::Running selected transform method: LOG
2026-03-12 19:15:31.71 INFO::Fitting model to feature number 1, a
2026-03-12 19:15:31.71 INFO::Fitting model to feature number 2, b
2026-03-12 19:15:31.71 INFO::Fitting model to feature number 3, c
2026-03-12 19:15:31.75 INFO::Creating output folder
2026-03-12 19:15:31.76 INFO::Creating fits folder
2026-03-12 19:15:31.76 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13541f68645/fits/residuals_linear.rds
2026-03-12 19:15:31.77 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13541f68645/fits/fitted_linear.rds
2026-03-12 19:15:31.77 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13541f68645/fits/residuals_logistic.rds
2026-03-12 19:15:31.77 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13541f68645/fits/fitted_logistic.rds
2026-03-12 19:15:31.77 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmplTRxDr/file13541f68645/all_results.tsv
2026-03-12 19:15:31.78 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//RtmplTRxDr/file13541f68645/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
144.741 4.639 156.986
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 6.997 | 0.471 | 7.719 | |
| maaslin_check_arguments | 0.058 | 0.002 | 0.062 | |
| maaslin_check_formula | 0.062 | 0.004 | 0.068 | |
| maaslin_compute_formula | 0.072 | 0.004 | 0.077 | |
| maaslin_contrast_test | 6.914 | 0.612 | 7.709 | |
| maaslin_filter | 0.252 | 0.024 | 0.284 | |
| maaslin_fit | 5.035 | 0.553 | 5.790 | |
| maaslin_log_arguments | 0.060 | 0.004 | 0.064 | |
| maaslin_normalize | 0.136 | 0.011 | 0.167 | |
| maaslin_plot_results | 17.481 | 0.847 | 19.161 | |
| maaslin_plot_results_from_output | 17.651 | 0.732 | 19.139 | |
| maaslin_process_metadata | 0.235 | 0.024 | 0.286 | |
| maaslin_read_data | 0.057 | 0.004 | 0.065 | |
| maaslin_reorder_data | 0.068 | 0.003 | 0.085 | |
| maaslin_transform | 0.304 | 0.032 | 0.357 | |
| maaslin_write_results | 5.794 | 0.553 | 6.564 | |
| maaslin_write_results_lefse_format | 5.937 | 0.489 | 6.751 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.002 | 0.000 | 0.002 | |