William Nickols
| Snapshot Date: 2026-03-08 13:40 -0400 (Sun, 08 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 2026-03-09 11:34 -0400 (Mon, 09 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" | 4508 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" | 3381 |
| 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: 2026-03-08 17:11:22 -0400 (Sun, 08 Mar 2026) |
| EndedAt: 2026-03-08 17:15:08 -0400 (Sun, 08 Mar 2026) |
| EllapsedTime: 226.3 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) (2026-02-28 r89501)
* 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
* current time: 2026-03-08 21:11:22 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 16.167 0.472 16.708
maaslin_plot_results 15.716 0.609 16.384
maaslin3 6.167 0.357 6.545
maaslin_contrast_test 5.902 0.562 6.481
maaslin_write_results_lefse_format 5.373 0.449 5.828
maaslin_write_results 5.051 0.374 5.497
maaslin_fit 4.596 0.447 5.107
* 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) (2026-02-28 r89501) -- "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")
2026-03-08 17:12:49.07 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:12:49.09 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:12:49.13 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:12:49.14 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:12:49.15 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:12:49.18 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:12:49.18 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:12:49.19 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:12:49.22 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:12:49.23 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:12:49.24 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:12:49.26 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:12:49.26 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:12:49.28 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:12:49.30 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:12:54.22 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:12:54.25 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:12:54.28 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:12:54.29 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:12:54.30 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:12:54.33 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:12:54.33 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:12:54.34 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:12:54.37 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:12:54.37 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:12:54.39 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:12:54.40 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:12:54.41 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:12:54.42 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:12:54.45 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:12:56.028 R[83386:119401087] XType: Using static font registry.
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-03-08 17:13:05.20 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:05.23 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:05.26 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:05.26 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:05.28 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:05.31 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:05.31 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:05.31 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:05.35 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:05.35 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:05.37 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:05.40 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:05.40 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:05.42 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:05.44 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:10.09 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:10.13 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:10.16 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:10.17 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:10.18 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:10.21 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:10.21 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:10.21 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:10.24 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:10.25 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:10.26 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:10.28 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:10.28 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:10.30 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:10.32 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:10.40 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/residuals_linear.rds
2026-03-08 17:13:10.43 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/fitted_linear.rds
2026-03-08 17:13:10.47 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/residuals_logistic.rds
2026-03-08 17:13:10.64 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/fitted_logistic.rds
2026-03-08 17:13:19.55 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:19.58 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:19.60 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:19.61 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:19.62 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:19.65 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:19.65 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:19.66 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:19.71 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:19.71 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:19.73 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:19.75 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:19.75 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:19.77 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:19.79 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:24.61 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:24.64 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:24.67 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:24.68 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:24.69 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:24.71 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:24.72 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:24.72 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:24.76 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:24.76 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:24.79 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:24.81 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:24.81 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:24.82 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:24.85 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:24.92 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/residuals_linear.rds
2026-03-08 17:13:24.95 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/fitted_linear.rds
2026-03-08 17:13:24.98 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/residuals_logistic.rds
2026-03-08 17:13:25.15 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/fitted_logistic.rds
2026-03-08 17:13:33.36 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:33.39 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:33.42 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:33.43 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:33.44 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:33.47 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:33.47 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:33.48 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:33.51 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:33.52 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:33.53 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:33.55 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:33.55 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:33.57 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:33.59 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:38.33 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:38.36 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:38.39 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:38.40 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:38.41 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:38.44 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:38.44 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:38.44 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:38.48 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:38.48 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:38.50 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:38.52 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:38.52 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:38.56 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:38.59 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:38.65 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/residuals_linear.rds
2026-03-08 17:13:38.68 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/fitted_linear.rds
2026-03-08 17:13:38.71 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/residuals_logistic.rds
2026-03-08 17:13:38.88 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba12467cfd/fits/fitted_logistic.rds
2026-03-08 17:13:46.60 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:46.63 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:46.65 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:46.66 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:46.67 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:46.69 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:46.69 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:46.70 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:46.73 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:46.73 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:46.75 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:46.76 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:46.76 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:46.79 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:46.81 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:13:51.40 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:13:51.43 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:13:51.46 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:13:51.46 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:13:51.48 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:13:51.51 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:13:51.51 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:13:51.51 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:13:51.55 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:13:51.56 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:13:51.58 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:13:51.59 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:13:51.60 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:13:51.61 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:13:51.67 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:14:00.40 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:04.14 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:13.36 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:17.19 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:17.38 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_linear.rds
2026-03-08 17:14:17.42 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_linear.rds
2026-03-08 17:14:17.44 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_logistic.rds
2026-03-08 17:14:17.48 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_logistic.rds
2026-03-08 17:14:27.09 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:29.07 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:29.17 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_linear.rds
2026-03-08 17:14:29.21 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_linear.rds
2026-03-08 17:14:29.25 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_logistic.rds
2026-03-08 17:14:29.31 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_logistic.rds
2026-03-08 17:14:36.90 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:39.43 WARNING::Fitting problem for feature 124 returning NA
2026-03-08 17:14:39.52 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_linear.rds
2026-03-08 17:14:39.55 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_linear.rds
2026-03-08 17:14:39.57 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_logistic.rds
2026-03-08 17:14:39.61 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_logistic.rds
2026-03-08 17:14:46.88 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:14:46.91 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:14:46.94 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:14:46.95 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:14:46.96 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:14:46.99 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:14:46.99 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:14:46.99 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:14:47.03 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:14:47.03 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:14:47.05 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:14:47.09 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:14:47.09 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:14:47.11 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:14:47.13 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:14:52.06 WARNING::Fitting problem for feature 50 returning NA
2026-03-08 17:14:52.09 WARNING::Fitting problem for feature 62 returning NA
2026-03-08 17:14:52.11 WARNING::Fitting problem for feature 74 returning NA
2026-03-08 17:14:52.12 WARNING::Fitting problem for feature 78 returning NA
2026-03-08 17:14:52.13 WARNING::Fitting problem for feature 84 returning NA
2026-03-08 17:14:52.16 WARNING::Fitting problem for feature 96 returning NA
2026-03-08 17:14:52.16 WARNING::Fitting problem for feature 97 returning NA
2026-03-08 17:14:52.17 WARNING::Fitting problem for feature 99 returning NA
2026-03-08 17:14:52.22 WARNING::Fitting problem for feature 114 returning NA
2026-03-08 17:14:52.22 WARNING::Fitting problem for feature 115 returning NA
2026-03-08 17:14:52.24 WARNING::Fitting problem for feature 123 returning NA
2026-03-08 17:14:52.25 WARNING::Fitting problem for feature 130 returning NA
2026-03-08 17:14:52.26 WARNING::Fitting problem for feature 132 returning NA
2026-03-08 17:14:52.27 WARNING::Fitting problem for feature 139 returning NA
2026-03-08 17:14:52.30 WARNING::Fitting problem for feature 150 returning NA
2026-03-08 17:14:52.38 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_linear.rds
2026-03-08 17:14:52.41 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_linear.rds
2026-03-08 17:14:52.45 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/residuals_logistic.rds
2026-03-08 17:14:52.62 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba649ae479/fits/fitted_logistic.rds
2026-03-08 17:15:00.68 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-08 17:15:00.69 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-08 17:15:00.69 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-08 17:15:00.71 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-08 17:15:00.72 ERROR::Effect name not found in metadata: d
2026-03-08 17:15:00.72 ERROR::No user formula provided
2026-03-08 17:15:00.73 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-08 17:15:00.74 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-08 17:15:01.73 INFO::Writing function arguments to log file
2026-03-08 17:15:01.74 INFO::Verifying options selected are valid
2026-03-08 17:15:02.63 INFO::Writing function arguments to log file
2026-03-08 17:15:02.64 INFO::Verifying options selected are valid
2026-03-08 17:15:02.64 INFO::Determining format of input files
2026-03-08 17:15:02.64 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-08 17:15:02.64 INFO::Running selected normalization method: TSS
2026-03-08 17:15:02.64 INFO::Creating output feature tables folder
2026-03-08 17:15:02.64 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/features/data_norm.tsv
2026-03-08 17:15:02.64 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-08 17:15:02.64 INFO::Total samples in data: 16
2026-03-08 17:15:02.64 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-08 17:15:02.64 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-08 17:15:02.64 INFO::Total filtered features: 0
2026-03-08 17:15:02.64 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-08 17:15:02.65 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-08 17:15:02.65 INFO::Filtered feature names from variance filtering:
2026-03-08 17:15:02.65 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/features/filtered_data.tsv
2026-03-08 17:15:02.65 INFO::Running selected transform method: LOG
2026-03-08 17:15:02.65 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/features/data_transformed.tsv
2026-03-08 17:15:02.65 INFO::Applying z-score to standardize continuous metadata
2026-03-08 17:15:02.65 INFO::Running the linear model component
2026-03-08 17:15:02.66 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:02.66 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:02.66 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:02.66 INFO::Counting total values for each feature
2026-03-08 17:15:02.66 INFO::Running the logistic model component
2026-03-08 17:15:02.67 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:02.67 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:02.67 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:02.68 INFO::Counting total values for each feature
2026-03-08 17:15:02.68 INFO::Re-running abundances for warn_prevalence
2026-03-08 17:15:02.68 INFO::Running selected normalization method: TSS
2026-03-08 17:15:02.68 INFO::Running selected transform method: LOG
2026-03-08 17:15:02.69 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:02.69 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:02.69 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:02.71 INFO::Creating fits folder
2026-03-08 17:15:02.71 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/fits/residuals_linear.rds
2026-03-08 17:15:02.71 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/fits/fitted_linear.rds
2026-03-08 17:15:02.71 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/fits/residuals_logistic.rds
2026-03-08 17:15:02.71 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/fits/fitted_logistic.rds
2026-03-08 17:15:02.71 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/all_results.tsv
2026-03-08 17:15:02.72 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//RtmpS0O4su/file145badae3760/significant_results.tsv
2026-03-08 17:15:02.72 INFO::Creating output figures folder
2026-03-08 17:15:02.72 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/figures/summary_plot.pdf
2026-03-08 17:15:03.31 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/figures
2026-03-08 17:15:03.31 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-08 17:15:03.31 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-08 17:15:03.51 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/figures/summary_plot.pdf
2026-03-08 17:15:04.10 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145badae3760/figures
2026-03-08 17:15:04.10 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-08 17:15:04.10 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-08 17:15:04.29 INFO::Running the linear model component
2026-03-08 17:15:04.29 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:04.29 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:04.29 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:04.30 INFO::Counting total values for each feature
2026-03-08 17:15:04.30 INFO::Running the logistic model component
2026-03-08 17:15:04.30 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:04.30 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:04.30 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:04.31 INFO::Counting total values for each feature
2026-03-08 17:15:04.31 INFO::Re-running abundances for warn_prevalence
2026-03-08 17:15:04.31 INFO::Running selected normalization method: TSS
2026-03-08 17:15:04.31 INFO::Running selected transform method: LOG
2026-03-08 17:15:04.31 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:04.31 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:04.31 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:04.34 INFO::Creating output folder
2026-03-08 17:15:04.34 INFO::Creating output figures folder
2026-03-08 17:15:04.34 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba45d7bb74/figures/summary_plot.pdf
2026-03-08 17:15:04.92 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba45d7bb74/figures
2026-03-08 17:15:04.92 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-08 17:15:04.92 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-08 17:15:05.31 INFO::Applying z-score to standardize continuous metadata
2026-03-08 17:15:05.31 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-08 17:15:05.31 INFO::Bypass z-score application to metadata
2026-03-08 17:15:05.31 INFO::Bypass z-score application to metadata
2026-03-08 17:15:05.33 INFO::Determining format of input files
2026-03-08 17:15:05.33 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-08 17:15:05.33 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-08 17:15:05.33 INFO::Determining format of input files
2026-03-08 17:15:05.33 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-08 17:15:05.33 INFO::Input format is feature_specific_covariate samples as columns
2026-03-08 17:15:05.33 INFO::Determining format of input files
2026-03-08 17:15:05.33 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-08 17:15:05.34 INFO::Input format is feature_specific_covariate samples as columns
2026-03-08 17:15:05.34 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-08 17:15:05.34 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-08 17:15:05.34 INFO::Running selected transform method: LOG
2026-03-08 17:15:05.34 INFO::Creating output feature tables folder
2026-03-08 17:15:05.34 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba4f6d935/features/data_transformed.tsv
2026-03-08 17:15:05.34 INFO::Running selected transform method: LOG
2026-03-08 17:15:05.34 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba4f6d935/features/data_transformed.tsv
2026-03-08 17:15:05.34 INFO::Running selected transform method: PLOG
2026-03-08 17:15:05.34 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba4f6d935/features/data_transformed.tsv
2026-03-08 17:15:05.35 INFO::Running selected transform method: NONE
2026-03-08 17:15:05.35 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba4f6d935/features/data_transformed.tsv
2026-03-08 17:15:05.35 INFO::Running the linear model component
2026-03-08 17:15:05.35 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:05.35 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:05.35 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:05.36 INFO::Counting total values for each feature
2026-03-08 17:15:05.36 INFO::Running the logistic model component
2026-03-08 17:15:05.36 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:05.36 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:05.36 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:05.37 INFO::Counting total values for each feature
2026-03-08 17:15:05.37 INFO::Re-running abundances for warn_prevalence
2026-03-08 17:15:05.37 INFO::Running selected normalization method: TSS
2026-03-08 17:15:05.37 INFO::Running selected transform method: LOG
2026-03-08 17:15:05.37 INFO::Fitting model to feature number 1, a
2026-03-08 17:15:05.37 INFO::Fitting model to feature number 2, b
2026-03-08 17:15:05.37 INFO::Fitting model to feature number 3, c
2026-03-08 17:15:05.39 INFO::Creating output folder
2026-03-08 17:15:05.40 INFO::Creating fits folder
2026-03-08 17:15:05.40 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba6a2e291e/fits/residuals_linear.rds
2026-03-08 17:15:05.40 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba6a2e291e/fits/fitted_linear.rds
2026-03-08 17:15:05.40 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba6a2e291e/fits/residuals_logistic.rds
2026-03-08 17:15:05.40 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba6a2e291e/fits/fitted_logistic.rds
2026-03-08 17:15:05.40 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpS0O4su/file145ba6a2e291e/all_results.tsv
2026-03-08 17:15:05.40 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//RtmpS0O4su/file145ba6a2e291e/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
130.945 4.710 137.620
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 6.167 | 0.357 | 6.545 | |
| maaslin_check_arguments | 0.049 | 0.001 | 0.050 | |
| maaslin_check_formula | 0.050 | 0.004 | 0.053 | |
| maaslin_compute_formula | 0.051 | 0.004 | 0.055 | |
| maaslin_contrast_test | 5.902 | 0.562 | 6.481 | |
| maaslin_filter | 0.219 | 0.020 | 0.241 | |
| maaslin_fit | 4.596 | 0.447 | 5.107 | |
| maaslin_log_arguments | 0.056 | 0.003 | 0.059 | |
| maaslin_normalize | 0.126 | 0.010 | 0.140 | |
| maaslin_plot_results | 15.716 | 0.609 | 16.384 | |
| maaslin_plot_results_from_output | 16.167 | 0.472 | 16.708 | |
| maaslin_process_metadata | 0.243 | 0.015 | 0.259 | |
| maaslin_read_data | 0.057 | 0.003 | 0.061 | |
| maaslin_reorder_data | 0.068 | 0.004 | 0.071 | |
| maaslin_transform | 0.494 | 0.047 | 0.550 | |
| maaslin_write_results | 5.051 | 0.374 | 5.497 | |
| maaslin_write_results_lefse_format | 5.373 | 0.449 | 5.828 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |