William Nickols
| Snapshot Date: 2026-01-01 13:40 -0500 (Thu, 01 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-03 11:35 -0500 (Sat, 03 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4809 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1158/2332 | 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 | | ||||||||
|
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: 2026-01-01 20:40:21 -0500 (Thu, 01 Jan 2026) |
| EndedAt: 2026-01-01 20:45:43 -0500 (Thu, 01 Jan 2026) |
| EllapsedTime: 322.3 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) (2025-11-04 r88984)
* 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 Ventura 13.7.8
* 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 ... OK
* 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 17.369 0.713 19.117
maaslin_plot_results_from_output 17.161 0.651 19.057
maaslin3 8.326 0.554 9.387
maaslin_contrast_test 7.744 0.671 8.977
maaslin_write_results 6.121 0.626 7.213
maaslin_write_results_lefse_format 5.821 0.438 6.611
maaslin_fit 5.035 0.582 6.006
* 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: OK
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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2026-01-01 20:43:08.039881 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:08.071349 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:08.10373 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:08.112458 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:08.13092 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:08.1608 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:08.163039 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:08.167535 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:08.2075 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:08.209647 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:08.229035 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:08.247714 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:08.252843 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:08.268643 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:08.298086 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:43:15.508819 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:15.536841 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:15.562438 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:15.569838 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:15.581477 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:15.620524 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:15.622554 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:15.626577 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:15.663339 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:15.665494 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:15.686779 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:15.700649 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:15.704948 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:15.718915 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:15.746092 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:43:17.334 R[42935:618362264] XType: Using static font registry.
2026-01-01 20:43:25.781115 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:25.806941 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:25.83284 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:25.846397 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:25.858804 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:25.887618 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:25.889706 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:25.89374 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:25.926853 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:25.928977 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:25.946363 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:25.960121 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:25.96464 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:25.978244 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:26.002597 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:43:31.60667 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:31.63203 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:31.661288 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:31.669414 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:31.681271 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:31.7079 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:31.713894 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:31.718067 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:31.757634 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:31.760308 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:31.779096 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:31.793649 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:31.798625 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:31.817514 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:31.847032 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:43:31.935852 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/residuals_linear.rds
2026-01-01 20:43:31.975038 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/fitted_linear.rds
2026-01-01 20:43:32.0301 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/residuals_logistic.rds
2026-01-01 20:43:32.211235 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/fitted_logistic.rds
2026-01-01 20:43:42.278649 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:42.305507 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:42.338186 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:42.34626 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:42.358171 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:42.384743 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:42.386787 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:42.391994 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:42.428734 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:42.431307 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:42.45405 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:42.468686 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:42.472905 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:42.488504 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:42.513254 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:43:47.712953 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:47.743063 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:47.770426 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:47.777942 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:47.790275 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:47.817433 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:47.819994 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:47.826662 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:47.862381 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:47.864508 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:47.882173 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:47.898821 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:47.90373 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:47.922803 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:47.953682 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:43:48.049542 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/residuals_linear.rds
2026-01-01 20:43:48.085192 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/fitted_linear.rds
2026-01-01 20:43:48.124911 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/residuals_logistic.rds
2026-01-01 20:43:48.309965 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/fitted_logistic.rds
2026-01-01 20:43:57.296903 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:43:57.323546 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:43:57.355027 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:43:57.363756 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:43:57.377346 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:43:57.403885 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:43:57.405952 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:43:57.410142 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:43:57.450176 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:43:57.452583 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:43:57.470366 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:43:57.488184 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:43:57.493011 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:43:57.507771 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:43:57.544563 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:44:02.777107 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:44:02.808775 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:44:02.834963 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:44:02.842837 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:44:02.855042 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:44:02.885694 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:44:02.887827 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:44:02.892038 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:44:02.928362 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:44:02.93059 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:44:02.947449 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:44:02.965308 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:44:02.970908 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:44:02.987227 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:44:03.014021 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:44:03.096925 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/residuals_linear.rds
2026-01-01 20:44:03.130768 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/fitted_linear.rds
2026-01-01 20:44:03.1653 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/residuals_logistic.rds
2026-01-01 20:44:03.347976 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7649a91dc/fits/fitted_logistic.rds
2026-01-01 20:44:12.422174 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:44:12.450621 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:44:12.477325 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:44:12.485306 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:44:12.500964 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:44:12.530334 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:44:12.532542 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:44:12.537981 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:44:12.573454 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:44:12.575679 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:44:12.597219 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:44:12.613012 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:44:12.618726 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:44:12.634966 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:44:12.662593 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:44:18.018656 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:44:18.045754 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:44:18.071885 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:44:18.07941 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:44:18.102525 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:44:18.135136 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:44:18.1376 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:44:18.141975 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:44:18.176951 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:44:18.179114 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:44:18.20061 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:44:18.217087 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:44:18.222416 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:44:18.237764 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:44:18.263714 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:44:28.220798 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:44:32.362596 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:44:42.624732 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:44:46.637706 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:44:46.879267 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_linear.rds
2026-01-01 20:44:46.91321 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_linear.rds
2026-01-01 20:44:46.939316 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_logistic.rds
2026-01-01 20:44:46.983491 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_logistic.rds
2026-01-01 20:44:56.795602 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:44:59.568131 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:44:59.698871 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_linear.rds
2026-01-01 20:44:59.732803 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_linear.rds
2026-01-01 20:44:59.75632 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_logistic.rds
2026-01-01 20:44:59.800781 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_logistic.rds
2026-01-01 20:45:07.919388 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:45:10.63232 WARNING::Fitting problem for feature 124 returning NA
2026-01-01 20:45:10.766485 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_linear.rds
2026-01-01 20:45:10.802565 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_linear.rds
2026-01-01 20:45:10.827471 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_logistic.rds
2026-01-01 20:45:10.868657 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_logistic.rds
2026-01-01 20:45:18.69723 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:45:18.724722 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:45:18.753451 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:45:18.763009 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:45:18.776356 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:45:18.80765 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:45:18.809912 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:45:18.814783 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:45:18.867241 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:45:18.869484 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:45:18.890385 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:45:18.904686 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:45:18.909114 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:45:18.922993 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:45:18.952033 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:45:24.133812 WARNING::Fitting problem for feature 50 returning NA
2026-01-01 20:45:24.170696 WARNING::Fitting problem for feature 62 returning NA
2026-01-01 20:45:24.200189 WARNING::Fitting problem for feature 74 returning NA
2026-01-01 20:45:24.208032 WARNING::Fitting problem for feature 78 returning NA
2026-01-01 20:45:24.219546 WARNING::Fitting problem for feature 84 returning NA
2026-01-01 20:45:24.246625 WARNING::Fitting problem for feature 96 returning NA
2026-01-01 20:45:24.249282 WARNING::Fitting problem for feature 97 returning NA
2026-01-01 20:45:24.25427 WARNING::Fitting problem for feature 99 returning NA
2026-01-01 20:45:24.291916 WARNING::Fitting problem for feature 114 returning NA
2026-01-01 20:45:24.294024 WARNING::Fitting problem for feature 115 returning NA
2026-01-01 20:45:24.311949 WARNING::Fitting problem for feature 123 returning NA
2026-01-01 20:45:24.328753 WARNING::Fitting problem for feature 130 returning NA
2026-01-01 20:45:24.334148 WARNING::Fitting problem for feature 132 returning NA
2026-01-01 20:45:24.351631 WARNING::Fitting problem for feature 139 returning NA
2026-01-01 20:45:24.378769 WARNING::Fitting problem for feature 150 returning NA
2026-01-01 20:45:24.49939 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_linear.rds
2026-01-01 20:45:24.533006 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_linear.rds
2026-01-01 20:45:24.567931 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/residuals_logistic.rds
2026-01-01 20:45:24.755284 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7255ab6c5/fits/fitted_logistic.rds
2026-01-01 20:45:33.449362 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-01-01 20:45:33.455213 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-01-01 20:45:33.459318 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-01-01 20:45:33.480512 ERROR::No fixed, group, or
ordered effects included in formula.
2026-01-01 20:45:33.487364 ERROR::Effect name not found in metadata: d
2026-01-01 20:45:33.492372 ERROR::No user formula provided
2026-01-01 20:45:33.50369 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-01-01 20:45:33.511308 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-01-01 20:45:34.733048 INFO::Writing function arguments to log file
2026-01-01 20:45:34.738715 INFO::Verifying options selected are valid
2026-01-01 20:45:35.681949 INFO::Writing function arguments to log file
2026-01-01 20:45:35.687676 INFO::Verifying options selected are valid
2026-01-01 20:45:35.688147 INFO::Determining format of input files
2026-01-01 20:45:35.688469 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-01 20:45:35.689298 INFO::Running selected normalization method: TSS
2026-01-01 20:45:35.691472 INFO::Creating output feature tables folder
2026-01-01 20:45:35.692031 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/features/data_norm.tsv
2026-01-01 20:45:35.692776 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-01-01 20:45:35.693139 INFO::Total samples in data: 16
2026-01-01 20:45:35.693446 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-01-01 20:45:35.693762 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-01-01 20:45:35.694416 INFO::Total filtered features: 0
2026-01-01 20:45:35.694767 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-01-01 20:45:35.695171 INFO::Total features filtered by non-zero variance filtering: 0
2026-01-01 20:45:35.695479 INFO::Filtered feature names from variance filtering:
2026-01-01 20:45:35.695785 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/features/filtered_data.tsv
2026-01-01 20:45:35.696384 INFO::Running selected transform method: LOG
2026-01-01 20:45:35.696796 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/features/data_transformed.tsv
2026-01-01 20:45:35.69743 INFO::Applying z-score to standardize continuous metadata
2026-01-01 20:45:35.699503 INFO::Running the linear model component
2026-01-01 20:45:35.704827 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:35.706427 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:35.707815 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:35.710251 INFO::Counting total values for each feature
2026-01-01 20:45:35.710913 INFO::Running the logistic model component
2026-01-01 20:45:35.720457 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:35.723328 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:35.72611 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:35.729281 INFO::Counting total values for each feature
2026-01-01 20:45:35.730135 INFO::Re-running abundances for warn_prevalence
2026-01-01 20:45:35.73054 INFO::Running selected normalization method: TSS
2026-01-01 20:45:35.731068 INFO::Running selected transform method: LOG
2026-01-01 20:45:35.736515 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:35.738066 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:35.739425 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:35.770736 INFO::Creating fits folder
2026-01-01 20:45:35.771429 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/fits/residuals_linear.rds
2026-01-01 20:45:35.772054 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/fits/fitted_linear.rds
2026-01-01 20:45:35.772602 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/fits/residuals_logistic.rds
2026-01-01 20:45:35.773137 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/fits/fitted_logistic.rds
2026-01-01 20:45:35.774239 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/all_results.tsv
2026-01-01 20:45:35.775036 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//RtmpdMHrTc/filea7b732aaeb5d/significant_results.tsv
2026-01-01 20:45:35.775658 INFO::Creating output figures folder
2026-01-01 20:45:35.776215 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/figures/summary_plot.pdf
2026-01-01 20:45:36.440519 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/figures
2026-01-01 20:45:36.441495 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-01 20:45:36.443957 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-01 20:45:36.65187 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/figures/summary_plot.pdf
2026-01-01 20:45:37.29019 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b732aaeb5d/figures
2026-01-01 20:45:37.290895 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-01 20:45:37.293037 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-01 20:45:37.508185 INFO::Running the linear model component
2026-01-01 20:45:37.511741 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:37.513653 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:37.515234 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:37.518075 INFO::Counting total values for each feature
2026-01-01 20:45:37.518735 INFO::Running the logistic model component
2026-01-01 20:45:37.521463 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:37.523573 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:37.525285 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:37.528019 INFO::Counting total values for each feature
2026-01-01 20:45:37.528691 INFO::Re-running abundances for warn_prevalence
2026-01-01 20:45:37.528926 INFO::Running selected normalization method: TSS
2026-01-01 20:45:37.529354 INFO::Running selected transform method: LOG
2026-01-01 20:45:37.531952 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:37.533221 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:37.534369 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:37.561289 INFO::Creating output folder
2026-01-01 20:45:37.56171 INFO::Creating output figures folder
2026-01-01 20:45:37.562131 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7ec7e323/figures/summary_plot.pdf
2026-01-01 20:45:38.207614 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b7ec7e323/figures
2026-01-01 20:45:38.208246 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-01 20:45:38.210384 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-01 20:45:38.633006 INFO::Applying z-score to standardize continuous metadata
2026-01-01 20:45:38.6357 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-01-01 20:45:38.635978 INFO::Bypass z-score application to metadata
2026-01-01 20:45:38.636762 INFO::Bypass z-score application to metadata
2026-01-01 20:45:38.643508 INFO::Determining format of input files
2026-01-01 20:45:38.643818 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-01 20:45:38.644067 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-01-01 20:45:38.646322 INFO::Determining format of input files
2026-01-01 20:45:38.646646 INFO::Input format is data samples as columns and metadata samples as rows
2026-01-01 20:45:38.647034 INFO::Input format is feature_specific_covariate samples as columns
2026-01-01 20:45:38.649587 INFO::Determining format of input files
2026-01-01 20:45:38.649865 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-01 20:45:38.65016 INFO::Input format is feature_specific_covariate samples as columns
2026-01-01 20:45:38.650607 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-01-01 20:45:38.650822 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-01-01 20:45:38.65467 INFO::Running selected transform method: LOG
2026-01-01 20:45:38.655014 INFO::Creating output feature tables folder
2026-01-01 20:45:38.655392 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b75d3b2cc1/features/data_transformed.tsv
2026-01-01 20:45:38.656761 INFO::Running selected transform method: LOG
2026-01-01 20:45:38.657085 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b75d3b2cc1/features/data_transformed.tsv
2026-01-01 20:45:38.658287 INFO::Running selected transform method: PLOG
2026-01-01 20:45:38.65877 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b75d3b2cc1/features/data_transformed.tsv
2026-01-01 20:45:38.659739 INFO::Running selected transform method: NONE
2026-01-01 20:45:38.659979 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b75d3b2cc1/features/data_transformed.tsv
2026-01-01 20:45:38.662882 INFO::Running the linear model component
2026-01-01 20:45:38.665664 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:38.667057 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:38.668253 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:38.670567 INFO::Counting total values for each feature
2026-01-01 20:45:38.671128 INFO::Running the logistic model component
2026-01-01 20:45:38.673854 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:38.676173 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:38.67838 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:38.681797 INFO::Counting total values for each feature
2026-01-01 20:45:38.682603 INFO::Re-running abundances for warn_prevalence
2026-01-01 20:45:38.682907 INFO::Running selected normalization method: TSS
2026-01-01 20:45:38.683442 INFO::Running selected transform method: LOG
2026-01-01 20:45:38.686781 INFO::Fitting model to feature number 1, a
2026-01-01 20:45:38.688343 INFO::Fitting model to feature number 2, b
2026-01-01 20:45:38.689813 INFO::Fitting model to feature number 3, c
2026-01-01 20:45:38.723153 INFO::Creating output folder
2026-01-01 20:45:38.723643 INFO::Creating fits folder
2026-01-01 20:45:38.723997 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b757f762b8/fits/residuals_linear.rds
2026-01-01 20:45:38.724502 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b757f762b8/fits/fitted_linear.rds
2026-01-01 20:45:38.724924 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b757f762b8/fits/residuals_logistic.rds
2026-01-01 20:45:38.725321 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b757f762b8/fits/fitted_logistic.rds
2026-01-01 20:45:38.726227 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdMHrTc/filea7b757f762b8/all_results.tsv
2026-01-01 20:45:38.726862 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//RtmpdMHrTc/filea7b757f762b8/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.009 4.141 155.871
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.326 | 0.554 | 9.387 | |
| maaslin_check_arguments | 0.063 | 0.001 | 0.065 | |
| maaslin_check_formula | 0.063 | 0.005 | 0.074 | |
| maaslin_compute_formula | 0.070 | 0.005 | 0.080 | |
| maaslin_contrast_test | 7.744 | 0.671 | 8.977 | |
| maaslin_filter | 0.234 | 0.019 | 0.282 | |
| maaslin_fit | 5.035 | 0.582 | 6.006 | |
| maaslin_log_arguments | 0.056 | 0.003 | 0.064 | |
| maaslin_normalize | 0.127 | 0.013 | 0.160 | |
| maaslin_plot_results | 17.369 | 0.713 | 19.117 | |
| maaslin_plot_results_from_output | 17.161 | 0.651 | 19.057 | |
| maaslin_process_metadata | 0.237 | 0.020 | 0.287 | |
| maaslin_read_data | 0.056 | 0.003 | 0.058 | |
| maaslin_reorder_data | 0.082 | 0.006 | 0.104 | |
| maaslin_transform | 0.285 | 0.031 | 0.334 | |
| maaslin_write_results | 6.121 | 0.626 | 7.213 | |
| maaslin_write_results_lefse_format | 5.821 | 0.438 | 6.611 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.002 | 0.001 | 0.001 | |