William Nickols
| Snapshot Date: 2026-02-23 13:45 -0500 (Mon, 23 Feb 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-24 11:57 -0500 (Tue, 24 Feb 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" | 4891 |
| 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: 2026-02-24 00:54:23 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 01:16:16 -0500 (Tue, 24 Feb 2026) |
| EllapsedTime: 1312.5 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 43.832 0.246 44.037
maaslin_plot_results_from_output 43.116 0.318 43.440
maaslin3 20.662 0.568 21.231
maaslin_contrast_test 19.272 0.487 19.761
maaslin_write_results_lefse_format 14.972 0.199 15.225
maaslin_write_results 14.016 0.090 14.106
maaslin_fit 12.779 0.095 12.875
* 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")
2026-02-24 01:00:43.333155 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:00:43.422188 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:00:43.518162 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:00:43.539914 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:00:43.573925 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:00:43.649261 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:00:43.661221 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:00:43.673029 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:00:43.766784 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:00:43.772095 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:00:43.821762 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:00:43.869843 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:00:43.881721 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:00:43.921855 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:00:43.992558 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:00:59.945427 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:01:00.020205 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:01:00.092972 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:01:00.114519 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:01:00.148284 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:01:00.236216 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:01:00.241579 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:01:00.253472 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:01:00.347226 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:01:00.352418 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:01:00.401418 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:01:00.441118 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:01:00.452648 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:01:00.491669 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:01:00.559722 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:01:25.064859 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:01:25.141004 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:01:25.216267 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:01:25.238641 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:01:25.272965 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:01:25.348665 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:01:25.353967 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:01:25.36597 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:01:25.461728 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:01:25.467243 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:01:25.516881 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:01:25.565905 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:01:25.578974 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:01:25.623316 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:01:25.699204 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:01:38.299027 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:01:38.415271 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:01:38.496201 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:01:38.518881 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:01:38.555588 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:01:38.63556 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:01:38.64138 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:01:38.654107 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:01:38.756247 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:01:38.762255 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:01:38.813459 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:01:38.853994 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:01:38.866369 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:01:38.906566 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:01:38.975032 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:01:39.178136 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/residuals_linear.rds
2026-02-24 01:01:39.239419 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/fitted_linear.rds
2026-02-24 01:01:39.302434 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/residuals_logistic.rds
2026-02-24 01:01:39.60299 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/fitted_logistic.rds
2026-02-24 01:02:02.462548 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:02:02.545164 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:02:02.661622 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:02:02.686021 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:02:02.722327 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:02:02.803168 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:02:02.808594 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:02:02.82078 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:02:02.922345 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:02:02.928317 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:02:02.982776 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:02:03.024731 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:02:03.037268 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:02:03.081013 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:02:03.157376 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:02:14.981186 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:02:15.058232 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:02:15.135561 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:02:15.157313 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:02:15.191854 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:02:15.269142 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:02:15.274752 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:02:15.286925 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:02:15.387804 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:02:15.393354 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:02:15.443344 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:02:15.483686 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:02:15.496141 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:02:15.538299 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:02:15.609844 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:02:15.817215 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/residuals_linear.rds
2026-02-24 01:02:15.878499 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/fitted_linear.rds
2026-02-24 01:02:15.94173 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/residuals_logistic.rds
2026-02-24 01:02:16.240767 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/fitted_logistic.rds
2026-02-24 01:02:37.652059 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:02:37.732262 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:02:37.810887 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:02:37.834865 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:02:37.873366 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:02:37.98755 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:02:37.99328 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:02:38.005719 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:02:38.102307 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:02:38.10794 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:02:38.158801 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:02:38.199434 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:02:38.211593 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:02:38.253001 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:02:38.325426 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:02:50.530064 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:02:50.611598 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:02:50.692065 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:02:50.715276 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:02:50.75197 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:02:50.832801 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:02:50.838267 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:02:50.850527 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:02:50.946329 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:02:50.951956 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:02:51.002987 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:02:51.04374 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:02:51.055652 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:02:51.09658 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:02:51.166478 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:02:51.372915 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/residuals_linear.rds
2026-02-24 01:02:51.434505 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/fitted_linear.rds
2026-02-24 01:02:51.497653 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/residuals_logistic.rds
2026-02-24 01:02:51.797826 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a46c826714/fits/fitted_logistic.rds
2026-02-24 01:03:13.466691 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:03:13.542753 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:03:13.617041 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:03:13.639057 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:03:13.674003 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:03:13.750566 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:03:13.756266 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:03:13.768733 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:03:13.868166 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:03:13.873825 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:03:13.926946 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:03:13.96857 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:03:13.980671 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:03:14.022607 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:03:14.093835 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:03:26.208393 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:03:26.290534 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:03:26.371088 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:03:26.394624 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:03:26.431435 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:03:26.514944 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:03:26.520551 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:03:26.533202 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:03:26.63874 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:03:26.645171 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:03:26.698177 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:03:26.740289 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:03:26.752223 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:03:26.795161 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:03:26.867803 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:03:51.652218 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:04:01.819431 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:04:27.198257 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:04:36.982262 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:04:37.590469 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_linear.rds
2026-02-24 01:04:37.652195 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_linear.rds
2026-02-24 01:04:37.69105 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_logistic.rds
2026-02-24 01:04:37.760019 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_logistic.rds
2026-02-24 01:05:01.214222 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:05:07.675697 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:05:07.984018 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_linear.rds
2026-02-24 01:05:08.046717 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_linear.rds
2026-02-24 01:05:08.085966 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_logistic.rds
2026-02-24 01:05:08.15737 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_logistic.rds
2026-02-24 01:05:26.926438 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:05:34.110253 WARNING::Fitting problem for feature 124 returning NA
2026-02-24 01:05:34.488248 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_linear.rds
2026-02-24 01:05:34.551075 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_linear.rds
2026-02-24 01:05:34.590557 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_logistic.rds
2026-02-24 01:05:34.662646 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_logistic.rds
2026-02-24 01:05:54.153433 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:05:54.243784 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:05:54.333272 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:05:54.361841 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:05:54.402654 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:05:54.524896 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:05:54.530795 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:05:54.544027 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:05:54.648299 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:05:54.654036 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:05:54.707246 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:05:54.75062 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:05:54.763275 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:05:54.80646 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:05:54.880329 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:06:07.879179 WARNING::Fitting problem for feature 50 returning NA
2026-02-24 01:06:07.961422 WARNING::Fitting problem for feature 62 returning NA
2026-02-24 01:06:08.04337 WARNING::Fitting problem for feature 74 returning NA
2026-02-24 01:06:08.068861 WARNING::Fitting problem for feature 78 returning NA
2026-02-24 01:06:08.109997 WARNING::Fitting problem for feature 84 returning NA
2026-02-24 01:06:08.200478 WARNING::Fitting problem for feature 96 returning NA
2026-02-24 01:06:08.206765 WARNING::Fitting problem for feature 97 returning NA
2026-02-24 01:06:08.220583 WARNING::Fitting problem for feature 99 returning NA
2026-02-24 01:06:08.331691 WARNING::Fitting problem for feature 114 returning NA
2026-02-24 01:06:08.338285 WARNING::Fitting problem for feature 115 returning NA
2026-02-24 01:06:08.394501 WARNING::Fitting problem for feature 123 returning NA
2026-02-24 01:06:08.439297 WARNING::Fitting problem for feature 130 returning NA
2026-02-24 01:06:08.452312 WARNING::Fitting problem for feature 132 returning NA
2026-02-24 01:06:08.49497 WARNING::Fitting problem for feature 139 returning NA
2026-02-24 01:06:08.573435 WARNING::Fitting problem for feature 150 returning NA
2026-02-24 01:06:08.863794 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_linear.rds
2026-02-24 01:06:08.925791 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_linear.rds
2026-02-24 01:06:08.988614 WARNING::Deleting existing residuals file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/residuals_logistic.rds
2026-02-24 01:06:09.290263 WARNING::Deleting existing fitted file: /tmp/RtmpFnUvGg/file2566a47e736404/fits/fitted_logistic.rds
2026-02-24 01:06:30.662228 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-24 01:06:30.680031 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-24 01:06:30.691992 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-24 01:06:30.743583 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-24 01:06:30.760465 ERROR::Effect name not found in metadata: d
2026-02-24 01:06:30.77196 ERROR::No user formula provided
2026-02-24 01:06:30.803492 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-24 01:06:30.815668 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-24 01:06:33.683409 INFO::Writing function arguments to log file
2026-02-24 01:06:33.698265 INFO::Verifying options selected are valid
2026-02-24 01:06:36.061789 INFO::Writing function arguments to log file
2026-02-24 01:06:36.074307 INFO::Verifying options selected are valid
2026-02-24 01:06:36.075429 INFO::Determining format of input files
2026-02-24 01:06:36.07642 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-24 01:06:36.078774 INFO::Running selected normalization method: TSS
2026-02-24 01:06:36.080218 INFO::Creating output feature tables folder
2026-02-24 01:06:36.081156 INFO::Writing normalized data to file /tmp/RtmpFnUvGg/file2566a44a68e562/features/data_norm.tsv
2026-02-24 01:06:36.082616 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-24 01:06:36.083496 INFO::Total samples in data: 16
2026-02-24 01:06:36.084352 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-24 01:06:36.085203 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-24 01:06:36.087097 INFO::Total filtered features: 0
2026-02-24 01:06:36.088045 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-24 01:06:36.089194 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-24 01:06:36.090137 INFO::Filtered feature names from variance filtering:
2026-02-24 01:06:36.091011 INFO::Writing filtered data to file /tmp/RtmpFnUvGg/file2566a44a68e562/features/filtered_data.tsv
2026-02-24 01:06:36.092484 INFO::Running selected transform method: LOG
2026-02-24 01:06:36.093688 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpFnUvGg/file2566a44a68e562/features/data_transformed.tsv
2026-02-24 01:06:36.095321 INFO::Applying z-score to standardize continuous metadata
2026-02-24 01:06:36.100034 INFO::Running the linear model component
2026-02-24 01:06:36.114033 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:36.118689 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:36.122836 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:36.129972 INFO::Counting total values for each feature
2026-02-24 01:06:36.131744 INFO::Running the logistic model component
2026-02-24 01:06:36.145632 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:36.152186 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:36.158262 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:36.167063 INFO::Counting total values for each feature
2026-02-24 01:06:36.169208 INFO::Re-running abundances for warn_prevalence
2026-02-24 01:06:36.170155 INFO::Running selected normalization method: TSS
2026-02-24 01:06:36.171668 INFO::Running selected transform method: LOG
2026-02-24 01:06:36.185762 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:36.190171 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:36.194445 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:36.269823 INFO::Creating fits folder
2026-02-24 01:06:36.271095 INFO::Writing residuals to file /tmp/RtmpFnUvGg/file2566a44a68e562/fits/residuals_linear.rds
2026-02-24 01:06:36.272316 INFO::Writing fitted values to file /tmp/RtmpFnUvGg/file2566a44a68e562/fits/fitted_linear.rds
2026-02-24 01:06:36.273558 INFO::Writing residuals to file /tmp/RtmpFnUvGg/file2566a44a68e562/fits/residuals_logistic.rds
2026-02-24 01:06:36.27476 INFO::Writing fitted values to file /tmp/RtmpFnUvGg/file2566a44a68e562/fits/fitted_logistic.rds
2026-02-24 01:06:36.277141 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpFnUvGg/file2566a44a68e562/all_results.tsv
2026-02-24 01:06:36.278741 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/RtmpFnUvGg/file2566a44a68e562/significant_results.tsv
2026-02-24 01:06:36.280062 INFO::Creating output figures folder
2026-02-24 01:06:36.281403 INFO::Writing summary plot of significant
results to file: /tmp/RtmpFnUvGg/file2566a44a68e562/figures/summary_plot.pdf
2026-02-24 01:06:37.914244 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpFnUvGg/file2566a44a68e562/figures
2026-02-24 01:06:37.916452 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-24 01:06:37.922073 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-24 01:06:38.503242 INFO::Writing summary plot of
significant results to file: /tmp/RtmpFnUvGg/file2566a44a68e562/figures/summary_plot.pdf
2026-02-24 01:06:40.171529 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpFnUvGg/file2566a44a68e562/figures
2026-02-24 01:06:40.173094 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-24 01:06:40.177971 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-24 01:06:40.73767 INFO::Running the linear model component
2026-02-24 01:06:40.747636 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:40.752401 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:40.757201 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:40.764929 INFO::Counting total values for each feature
2026-02-24 01:06:40.766743 INFO::Running the logistic model component
2026-02-24 01:06:40.775643 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:40.782415 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:40.78876 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:40.797996 INFO::Counting total values for each feature
2026-02-24 01:06:40.800082 INFO::Re-running abundances for warn_prevalence
2026-02-24 01:06:40.800872 INFO::Running selected normalization method: TSS
2026-02-24 01:06:40.802249 INFO::Running selected transform method: LOG
2026-02-24 01:06:40.811116 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:40.815671 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:40.81989 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:40.90334 INFO::Creating output folder
2026-02-24 01:06:40.904473 INFO::Creating output figures folder
2026-02-24 01:06:40.905889 INFO::Writing summary plot of significant
results to file: /tmp/RtmpFnUvGg/file2566a43a34477a/figures/summary_plot.pdf
2026-02-24 01:06:42.555239 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpFnUvGg/file2566a43a34477a/figures
2026-02-24 01:06:42.557266 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-24 01:06:42.5623 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-24 01:06:43.719589 INFO::Applying z-score to standardize continuous metadata
2026-02-24 01:06:43.72731 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-24 01:06:43.728248 INFO::Bypass z-score application to metadata
2026-02-24 01:06:43.731019 INFO::Bypass z-score application to metadata
2026-02-24 01:06:43.751639 INFO::Determining format of input files
2026-02-24 01:06:43.752677 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-24 01:06:43.753547 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-24 01:06:43.761254 INFO::Determining format of input files
2026-02-24 01:06:43.762384 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-24 01:06:43.763783 INFO::Input format is feature_specific_covariate samples as columns
2026-02-24 01:06:43.772201 INFO::Determining format of input files
2026-02-24 01:06:43.773146 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-24 01:06:43.774153 INFO::Input format is feature_specific_covariate samples as columns
2026-02-24 01:06:43.775806 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-24 01:06:43.776572 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-24 01:06:43.788452 INFO::Running selected transform method: LOG
2026-02-24 01:06:43.789826 INFO::Creating output feature tables folder
2026-02-24 01:06:43.790739 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpFnUvGg/file2566a457415eec/features/data_transformed.tsv
2026-02-24 01:06:43.794778 INFO::Running selected transform method: LOG
2026-02-24 01:06:43.795856 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpFnUvGg/file2566a457415eec/features/data_transformed.tsv
2026-02-24 01:06:43.800002 INFO::Running selected transform method: PLOG
2026-02-24 01:06:43.801556 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpFnUvGg/file2566a457415eec/features/data_transformed.tsv
2026-02-24 01:06:43.804577 INFO::Running selected transform method: NONE
2026-02-24 01:06:43.805307 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpFnUvGg/file2566a457415eec/features/data_transformed.tsv
2026-02-24 01:06:43.813107 INFO::Running the linear model component
2026-02-24 01:06:43.82202 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:43.82666 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:43.831108 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:43.83908 INFO::Counting total values for each feature
2026-02-24 01:06:43.840858 INFO::Running the logistic model component
2026-02-24 01:06:43.849536 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:43.856456 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:43.862957 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:43.871935 INFO::Counting total values for each feature
2026-02-24 01:06:43.874013 INFO::Re-running abundances for warn_prevalence
2026-02-24 01:06:43.874852 INFO::Running selected normalization method: TSS
2026-02-24 01:06:43.876227 INFO::Running selected transform method: LOG
2026-02-24 01:06:43.885172 INFO::Fitting model to feature number 1, a
2026-02-24 01:06:43.889745 INFO::Fitting model to feature number 2, b
2026-02-24 01:06:43.894459 INFO::Fitting model to feature number 3, c
2026-02-24 01:06:43.980278 INFO::Creating output folder
2026-02-24 01:06:43.981321 INFO::Creating fits folder
2026-02-24 01:06:43.982228 INFO::Writing residuals to file /tmp/RtmpFnUvGg/file2566a41b135019/fits/residuals_linear.rds
2026-02-24 01:06:43.983243 INFO::Writing fitted values to file /tmp/RtmpFnUvGg/file2566a41b135019/fits/fitted_linear.rds
2026-02-24 01:06:43.984496 INFO::Writing residuals to file /tmp/RtmpFnUvGg/file2566a41b135019/fits/residuals_logistic.rds
2026-02-24 01:06:43.98564 INFO::Writing fitted values to file /tmp/RtmpFnUvGg/file2566a41b135019/fits/fitted_logistic.rds
2026-02-24 01:06:43.988084 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpFnUvGg/file2566a41b135019/all_results.tsv
2026-02-24 01:06:43.989773 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/RtmpFnUvGg/file2566a41b135019/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
364.148 7.766 371.910
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.662 | 0.568 | 21.231 | |
| maaslin_check_arguments | 0.152 | 0.002 | 0.154 | |
| maaslin_check_formula | 0.185 | 0.002 | 0.187 | |
| maaslin_compute_formula | 0.160 | 0.000 | 0.161 | |
| maaslin_contrast_test | 19.272 | 0.487 | 19.761 | |
| maaslin_filter | 0.454 | 0.029 | 0.483 | |
| maaslin_fit | 12.779 | 0.095 | 12.875 | |
| maaslin_log_arguments | 0.139 | 0.003 | 0.142 | |
| maaslin_normalize | 0.272 | 0.007 | 0.279 | |
| maaslin_plot_results | 43.832 | 0.246 | 44.037 | |
| maaslin_plot_results_from_output | 43.116 | 0.318 | 43.440 | |
| maaslin_process_metadata | 0.489 | 0.029 | 0.518 | |
| maaslin_read_data | 0.136 | 0.000 | 0.136 | |
| maaslin_reorder_data | 0.138 | 0.000 | 0.138 | |
| maaslin_transform | 0.558 | 0.021 | 0.579 | |
| maaslin_write_results | 14.016 | 0.090 | 14.106 | |
| maaslin_write_results_lefse_format | 14.972 | 0.199 | 15.225 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |