William Nickols
| Snapshot Date: 2026-03-11 13:45 -0400 (Wed, 11 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-12 11:57 -0400 (Thu, 12 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4892 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-03-12 01:01:07 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 01:22:48 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 1300.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 loading without being on the library search path ... 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 43.563 0.326 43.852
maaslin_plot_results_from_output 43.256 0.396 43.656
maaslin3 20.757 0.513 21.271
maaslin_contrast_test 18.300 0.279 18.594
maaslin_write_results_lefse_format 14.374 0.074 14.451
maaslin_write_results 12.859 0.096 12.958
maaslin_fit 12.088 0.069 12.159
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 01:07:23.54642 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:07:23.633192 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:07:23.726351 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:07:23.748233 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:07:23.782575 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:07:23.859589 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:07:23.874625 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:07:23.886853 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:07:23.982028 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:07:23.987245 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:07:24.035679 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:07:24.082079 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:07:24.093694 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:07:24.132929 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:07:24.200958 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:07:39.891659 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:07:39.967459 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:07:40.046707 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:07:40.067914 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:07:40.101527 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:07:40.188576 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:07:40.193724 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:07:40.205182 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:07:40.298418 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:07:40.303636 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:07:40.35196 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:07:40.390644 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:07:40.401966 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:07:40.441238 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:07:40.509185 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:08:05.031566 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:08:05.110608 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:08:05.186875 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:08:05.209151 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:08:05.244928 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:08:05.32091 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:08:05.326457 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:08:05.339004 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:08:05.440384 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:08:05.446287 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:08:05.49955 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:08:05.540838 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:08:05.553066 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:08:05.594294 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:08:05.666374 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:08:18.728988 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:08:18.834263 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:08:18.91164 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:08:18.934324 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:08:18.97192 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:08:19.050104 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:08:19.055698 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:08:19.067893 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:08:19.162647 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:08:19.168152 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:08:19.218245 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:08:19.258223 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:08:19.270262 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:08:19.310519 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:08:19.380574 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:08:19.585356 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/residuals_linear.rds
2026-03-12 01:08:19.647199 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/fitted_linear.rds
2026-03-12 01:08:19.710842 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/residuals_logistic.rds
2026-03-12 01:08:20.010912 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/fitted_logistic.rds
2026-03-12 01:08:42.180083 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:08:42.258172 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:08:42.36725 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:08:42.390096 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:08:42.425694 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:08:42.501341 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:08:42.506539 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:08:42.517983 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:08:42.611846 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:08:42.617229 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:08:42.665229 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:08:42.704382 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:08:42.71607 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:08:42.756135 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:08:42.824415 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:08:54.921321 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:08:55.002115 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:08:55.07944 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:08:55.101149 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:08:55.13609 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:08:55.217177 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:08:55.222597 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:08:55.234473 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:08:55.330254 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:08:55.335663 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:08:55.386131 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:08:55.426655 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:08:55.438613 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:08:55.479805 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:08:55.551623 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:08:55.756413 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/residuals_linear.rds
2026-03-12 01:08:55.817409 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/fitted_linear.rds
2026-03-12 01:08:55.880141 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/residuals_logistic.rds
2026-03-12 01:08:56.179236 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/fitted_logistic.rds
2026-03-12 01:09:17.810708 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:09:17.900042 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:09:17.984624 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:09:18.009995 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:09:18.049659 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:09:18.168052 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:09:18.17465 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:09:18.188644 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:09:18.29299 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:09:18.298921 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:09:18.351593 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:09:18.394699 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:09:18.408024 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:09:18.452053 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:09:18.525221 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:09:30.556414 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:09:30.633863 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:09:30.708485 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:09:30.731243 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:09:30.767771 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:09:30.846766 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:09:30.85195 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:09:30.863393 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:09:30.956628 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:09:30.962028 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:09:31.011167 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:09:31.051398 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:09:31.063015 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:09:31.10286 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:09:31.172091 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:09:31.373536 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/residuals_linear.rds
2026-03-12 01:09:31.434331 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/fitted_linear.rds
2026-03-12 01:09:31.497134 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/residuals_logistic.rds
2026-03-12 01:09:31.796203 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a324c48669c/fits/fitted_logistic.rds
2026-03-12 01:09:53.157333 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:09:53.232084 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:09:53.306242 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:09:53.328275 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:09:53.362577 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:09:53.439152 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:09:53.444756 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:09:53.456691 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:09:53.552058 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:09:53.557564 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:09:53.60801 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:09:53.648574 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:09:53.6605 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:09:53.700926 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:09:53.771645 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:10:05.408886 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:10:05.482695 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:10:05.55701 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:10:05.578387 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:10:05.612302 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:10:05.687862 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:10:05.693147 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:10:05.704788 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:10:05.798901 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:10:05.80424 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:10:05.853778 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:10:05.894269 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:10:05.906479 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:10:05.947034 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:10:06.016382 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:10:31.740254 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:10:40.602293 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:11:05.852522 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:11:15.788278 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:11:16.416234 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_linear.rds
2026-03-12 01:11:16.477655 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_linear.rds
2026-03-12 01:11:16.516358 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_logistic.rds
2026-03-12 01:11:16.585311 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_logistic.rds
2026-03-12 01:11:39.642226 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:11:45.195276 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:11:45.519889 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_linear.rds
2026-03-12 01:11:45.581776 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_linear.rds
2026-03-12 01:11:45.620218 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_logistic.rds
2026-03-12 01:11:45.68913 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_logistic.rds
2026-03-12 01:12:04.723339 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:12:11.163203 WARNING::Fitting problem for feature 124 returning NA
2026-03-12 01:12:11.46508 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_linear.rds
2026-03-12 01:12:11.526578 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_linear.rds
2026-03-12 01:12:11.565286 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_logistic.rds
2026-03-12 01:12:11.634459 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_logistic.rds
2026-03-12 01:12:30.652618 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:12:30.730941 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:12:30.808548 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:12:30.831277 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:12:30.867144 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:12:30.945698 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:12:30.951185 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:12:30.987675 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:12:31.086184 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:12:31.091736 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:12:31.142519 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:12:31.182988 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:12:31.194993 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:12:31.235687 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:12:31.305202 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:12:41.977262 WARNING::Fitting problem for feature 50 returning NA
2026-03-12 01:12:42.053614 WARNING::Fitting problem for feature 62 returning NA
2026-03-12 01:12:42.127145 WARNING::Fitting problem for feature 74 returning NA
2026-03-12 01:12:42.149211 WARNING::Fitting problem for feature 78 returning NA
2026-03-12 01:12:42.184485 WARNING::Fitting problem for feature 84 returning NA
2026-03-12 01:12:42.260782 WARNING::Fitting problem for feature 96 returning NA
2026-03-12 01:12:42.266231 WARNING::Fitting problem for feature 97 returning NA
2026-03-12 01:12:42.278092 WARNING::Fitting problem for feature 99 returning NA
2026-03-12 01:12:42.374933 WARNING::Fitting problem for feature 114 returning NA
2026-03-12 01:12:42.3805 WARNING::Fitting problem for feature 115 returning NA
2026-03-12 01:12:42.43083 WARNING::Fitting problem for feature 123 returning NA
2026-03-12 01:12:42.470839 WARNING::Fitting problem for feature 130 returning NA
2026-03-12 01:12:42.482643 WARNING::Fitting problem for feature 132 returning NA
2026-03-12 01:12:42.522544 WARNING::Fitting problem for feature 139 returning NA
2026-03-12 01:12:42.590765 WARNING::Fitting problem for feature 150 returning NA
2026-03-12 01:12:42.857656 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_linear.rds
2026-03-12 01:12:42.918819 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_linear.rds
2026-03-12 01:12:42.981962 WARNING::Deleting existing residuals file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/residuals_logistic.rds
2026-03-12 01:12:43.280654 WARNING::Deleting existing fitted file: /tmp/Rtmpvg4ZBr/file218a321a2a9790/fits/fitted_logistic.rds
2026-03-12 01:13:03.883102 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-12 01:13:03.901598 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-12 01:13:03.914212 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-12 01:13:03.970534 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-12 01:13:03.987828 ERROR::Effect name not found in metadata: d
2026-03-12 01:13:03.999861 ERROR::No user formula provided
2026-03-12 01:13:04.033294 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-12 01:13:04.045188 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-12 01:13:06.901729 INFO::Writing function arguments to log file
2026-03-12 01:13:06.915929 INFO::Verifying options selected are valid
2026-03-12 01:13:09.245101 INFO::Writing function arguments to log file
2026-03-12 01:13:09.281971 INFO::Verifying options selected are valid
2026-03-12 01:13:09.283128 INFO::Determining format of input files
2026-03-12 01:13:09.284153 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-12 01:13:09.28663 INFO::Running selected normalization method: TSS
2026-03-12 01:13:09.288189 INFO::Creating output feature tables folder
2026-03-12 01:13:09.289172 INFO::Writing normalized data to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/features/data_norm.tsv
2026-03-12 01:13:09.290728 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-12 01:13:09.291645 INFO::Total samples in data: 16
2026-03-12 01:13:09.29249 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-12 01:13:09.293329 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-12 01:13:09.295301 INFO::Total filtered features: 0
2026-03-12 01:13:09.296248 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-12 01:13:09.297387 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-12 01:13:09.298324 INFO::Filtered feature names from variance filtering:
2026-03-12 01:13:09.299183 INFO::Writing filtered data to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/features/filtered_data.tsv
2026-03-12 01:13:09.30068 INFO::Running selected transform method: LOG
2026-03-12 01:13:09.30188 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/features/data_transformed.tsv
2026-03-12 01:13:09.303573 INFO::Applying z-score to standardize continuous metadata
2026-03-12 01:13:09.308218 INFO::Running the linear model component
2026-03-12 01:13:09.321914 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:09.326613 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:09.331017 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:09.338558 INFO::Counting total values for each feature
2026-03-12 01:13:09.340498 INFO::Running the logistic model component
2026-03-12 01:13:09.35411 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:09.360764 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:09.367042 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:09.376334 INFO::Counting total values for each feature
2026-03-12 01:13:09.37856 INFO::Re-running abundances for warn_prevalence
2026-03-12 01:13:09.379522 INFO::Running selected normalization method: TSS
2026-03-12 01:13:09.381051 INFO::Running selected transform method: LOG
2026-03-12 01:13:09.394793 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:09.399374 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:09.403685 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:09.483839 INFO::Creating fits folder
2026-03-12 01:13:09.485212 INFO::Writing residuals to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/fits/residuals_linear.rds
2026-03-12 01:13:09.486492 INFO::Writing fitted values to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/fits/fitted_linear.rds
2026-03-12 01:13:09.487819 INFO::Writing residuals to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/fits/residuals_logistic.rds
2026-03-12 01:13:09.489113 INFO::Writing fitted values to file /tmp/Rtmpvg4ZBr/file218a327e9bb101/fits/fitted_logistic.rds
2026-03-12 01:13:09.491807 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpvg4ZBr/file218a327e9bb101/all_results.tsv
2026-03-12 01:13:09.493602 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): /tmp/Rtmpvg4ZBr/file218a327e9bb101/significant_results.tsv
2026-03-12 01:13:09.494997 INFO::Creating output figures folder
2026-03-12 01:13:09.496394 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpvg4ZBr/file218a327e9bb101/figures/summary_plot.pdf
2026-03-12 01:13:11.105097 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpvg4ZBr/file218a327e9bb101/figures
2026-03-12 01:13:11.107044 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-12 01:13:11.112012 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-12 01:13:11.640393 INFO::Writing summary plot of
significant results to file: /tmp/Rtmpvg4ZBr/file218a327e9bb101/figures/summary_plot.pdf
2026-03-12 01:13:13.256135 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpvg4ZBr/file218a327e9bb101/figures
2026-03-12 01:13:13.257664 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-12 01:13:13.262473 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-12 01:13:13.781375 INFO::Running the linear model component
2026-03-12 01:13:13.790573 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:13.795059 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:13.79919 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:13.806135 INFO::Counting total values for each feature
2026-03-12 01:13:13.807782 INFO::Running the logistic model component
2026-03-12 01:13:13.81616 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:13.822348 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:13.828269 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:13.836942 INFO::Counting total values for each feature
2026-03-12 01:13:13.838891 INFO::Re-running abundances for warn_prevalence
2026-03-12 01:13:13.83964 INFO::Running selected normalization method: TSS
2026-03-12 01:13:13.840932 INFO::Running selected transform method: LOG
2026-03-12 01:13:13.849497 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:13.853541 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:13.857389 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:13.935248 INFO::Creating output folder
2026-03-12 01:13:13.936282 INFO::Creating output figures folder
2026-03-12 01:13:13.93761 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpvg4ZBr/file218a3214eea5bd/figures/summary_plot.pdf
2026-03-12 01:13:15.582316 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpvg4ZBr/file218a3214eea5bd/figures
2026-03-12 01:13:15.584074 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-12 01:13:15.589065 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-12 01:13:16.567291 INFO::Applying z-score to standardize continuous metadata
2026-03-12 01:13:16.574731 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-12 01:13:16.575592 INFO::Bypass z-score application to metadata
2026-03-12 01:13:16.578217 INFO::Bypass z-score application to metadata
2026-03-12 01:13:16.597317 INFO::Determining format of input files
2026-03-12 01:13:16.598269 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-12 01:13:16.599099 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-12 01:13:16.606521 INFO::Determining format of input files
2026-03-12 01:13:16.607502 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-12 01:13:16.608782 INFO::Input format is feature_specific_covariate samples as columns
2026-03-12 01:13:16.616968 INFO::Determining format of input files
2026-03-12 01:13:16.617861 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-12 01:13:16.618827 INFO::Input format is feature_specific_covariate samples as columns
2026-03-12 01:13:16.620409 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 01:13:16.621165 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 01:13:16.632588 INFO::Running selected transform method: LOG
2026-03-12 01:13:16.633662 INFO::Creating output feature tables folder
2026-03-12 01:13:16.634482 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpvg4ZBr/file218a324ac066b3/features/data_transformed.tsv
2026-03-12 01:13:16.638291 INFO::Running selected transform method: LOG
2026-03-12 01:13:16.639268 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpvg4ZBr/file218a324ac066b3/features/data_transformed.tsv
2026-03-12 01:13:16.643114 INFO::Running selected transform method: PLOG
2026-03-12 01:13:16.644671 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpvg4ZBr/file218a324ac066b3/features/data_transformed.tsv
2026-03-12 01:13:16.647551 INFO::Running selected transform method: NONE
2026-03-12 01:13:16.64828 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpvg4ZBr/file218a324ac066b3/features/data_transformed.tsv
2026-03-12 01:13:16.656077 INFO::Running the linear model component
2026-03-12 01:13:16.664608 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:16.669029 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:16.672936 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:16.679874 INFO::Counting total values for each feature
2026-03-12 01:13:16.68145 INFO::Running the logistic model component
2026-03-12 01:13:16.689796 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:16.696077 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:16.70207 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:16.711077 INFO::Counting total values for each feature
2026-03-12 01:13:16.713221 INFO::Re-running abundances for warn_prevalence
2026-03-12 01:13:16.714074 INFO::Running selected normalization method: TSS
2026-03-12 01:13:16.715504 INFO::Running selected transform method: LOG
2026-03-12 01:13:16.724155 INFO::Fitting model to feature number 1, a
2026-03-12 01:13:16.728376 INFO::Fitting model to feature number 2, b
2026-03-12 01:13:16.732279 INFO::Fitting model to feature number 3, c
2026-03-12 01:13:16.809659 INFO::Creating output folder
2026-03-12 01:13:16.810649 INFO::Creating fits folder
2026-03-12 01:13:16.811495 INFO::Writing residuals to file /tmp/Rtmpvg4ZBr/file218a3223d13233/fits/residuals_linear.rds
2026-03-12 01:13:16.812459 INFO::Writing fitted values to file /tmp/Rtmpvg4ZBr/file218a3223d13233/fits/fitted_linear.rds
2026-03-12 01:13:16.813539 INFO::Writing residuals to file /tmp/Rtmpvg4ZBr/file218a3223d13233/fits/residuals_logistic.rds
2026-03-12 01:13:16.814587 INFO::Writing fitted values to file /tmp/Rtmpvg4ZBr/file218a3223d13233/fits/fitted_logistic.rds
2026-03-12 01:13:16.81689 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpvg4ZBr/file218a3223d13233/all_results.tsv
2026-03-12 01:13:16.818363 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): /tmp/Rtmpvg4ZBr/file218a3223d13233/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
360.139 4.410 364.529
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.757 | 0.513 | 21.271 | |
| maaslin_check_arguments | 0.149 | 0.002 | 0.151 | |
| maaslin_check_formula | 0.133 | 0.002 | 0.135 | |
| maaslin_compute_formula | 0.136 | 0.000 | 0.136 | |
| maaslin_contrast_test | 18.300 | 0.279 | 18.594 | |
| maaslin_filter | 0.427 | 0.005 | 0.433 | |
| maaslin_fit | 12.088 | 0.069 | 12.159 | |
| maaslin_log_arguments | 0.130 | 0.001 | 0.131 | |
| maaslin_normalize | 0.283 | 0.002 | 0.285 | |
| maaslin_plot_results | 43.563 | 0.326 | 43.852 | |
| maaslin_plot_results_from_output | 43.256 | 0.396 | 43.656 | |
| maaslin_process_metadata | 0.446 | 0.013 | 0.458 | |
| maaslin_read_data | 0.126 | 0.002 | 0.128 | |
| maaslin_reorder_data | 0.132 | 0.000 | 0.132 | |
| maaslin_transform | 0.545 | 0.013 | 0.557 | |
| maaslin_write_results | 12.859 | 0.096 | 12.958 | |
| maaslin_write_results_lefse_format | 14.374 | 0.074 | 14.451 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |