William Nickols
| Snapshot Date: 2026-02-09 13:45 -0500 (Mon, 09 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 2026-02-12 11:58 -0500 (Thu, 12 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" | 4889 |
| 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: 2026-02-10 01:24:18 -0500 (Tue, 10 Feb 2026) |
| EndedAt: 2026-02-10 01:46:02 -0500 (Tue, 10 Feb 2026) |
| EllapsedTime: 1304.3 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 43.462 0.330 43.759
maaslin_plot_results_from_output 42.624 0.388 43.016
maaslin3 20.859 0.507 21.367
maaslin_contrast_test 19.191 0.362 19.555
maaslin_write_results 14.009 0.239 14.249
maaslin_write_results_lefse_format 14.100 0.053 14.155
maaslin_fit 12.948 0.093 13.042
* 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")
2026-02-10 01:30:35.72006 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:30:35.809238 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:30:35.903455 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:30:35.925245 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:30:35.959254 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:30:36.036578 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:30:36.049609 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:30:36.061801 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:30:36.157709 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:30:36.163152 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:30:36.213718 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:30:36.261199 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:30:36.273356 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:30:36.31458 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:30:36.388002 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:30:52.263893 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:30:52.338576 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:30:52.412083 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:30:52.433733 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:30:52.468092 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:30:52.568203 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:30:52.573866 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:30:52.586381 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:30:52.682113 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:30:52.687711 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:30:52.737311 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:30:52.777257 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:30:52.78947 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:30:52.830215 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:30:52.897186 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:31:17.379527 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:31:17.457326 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:31:17.53156 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:31:17.553272 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:31:17.588618 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:31:17.665072 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:31:17.670591 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:31:17.682603 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:31:17.780168 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:31:17.785685 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:31:17.836672 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:31:17.880158 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:31:17.894175 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:31:17.954012 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:31:18.030889 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:31:31.163489 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:31:31.265314 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:31:31.340801 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:31:31.362279 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:31:31.395963 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:31:31.470638 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:31:31.475967 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:31:31.487759 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:31:31.58227 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:31:31.587669 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:31:31.637 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:31:31.676794 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:31:31.688604 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:31:31.728611 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:31:31.796645 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:31:32.000672 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/residuals_linear.rds
2026-02-10 01:31:32.062415 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/fitted_linear.rds
2026-02-10 01:31:32.126208 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/residuals_logistic.rds
2026-02-10 01:31:32.429601 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/fitted_logistic.rds
2026-02-10 01:31:54.657735 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:31:54.738791 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:31:55.010044 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:31:55.033385 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:31:55.069684 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:31:55.150168 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:31:55.155883 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:31:55.168412 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:31:55.266137 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:31:55.27196 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:31:55.323621 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:31:55.366349 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:31:55.378776 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:31:55.421282 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:31:55.49333 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:32:07.400527 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:32:07.480939 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:32:07.560335 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:32:07.583235 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:32:07.618458 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:32:07.698563 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:32:07.704369 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:32:07.717117 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:32:07.820152 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:32:07.82582 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:32:07.878878 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:32:07.920198 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:32:07.933203 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:32:07.977349 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:32:08.052351 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:32:08.259913 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/residuals_linear.rds
2026-02-10 01:32:08.322167 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/fitted_linear.rds
2026-02-10 01:32:08.385108 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/residuals_logistic.rds
2026-02-10 01:32:08.685698 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/fitted_logistic.rds
2026-02-10 01:32:31.481487 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:32:31.563057 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:32:31.642582 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:32:31.665807 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:32:31.703854 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:32:31.788962 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:32:31.794927 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:32:31.807945 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:32:31.915484 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:32:31.921771 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:32:31.977395 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:32:32.02265 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:32:32.036444 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:32:32.080897 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:32:32.155045 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:32:43.37842 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:32:43.467224 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:32:43.553313 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:32:43.577356 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:32:43.613461 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:32:43.720345 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:32:43.728576 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:32:43.741862 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:32:43.848382 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:32:43.854705 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:32:43.907525 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:32:43.948771 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:32:43.960992 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:32:44.002484 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:32:44.073627 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:32:44.268605 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/residuals_linear.rds
2026-02-10 01:32:44.330144 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/fitted_linear.rds
2026-02-10 01:32:44.393407 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/residuals_logistic.rds
2026-02-10 01:32:44.692843 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe4621c483b7/fits/fitted_logistic.rds
2026-02-10 01:33:07.426984 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:33:07.537898 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:33:07.616394 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:33:07.638968 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:33:07.684738 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:33:07.766344 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:33:07.772138 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:33:07.784608 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:33:07.880524 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:33:07.886066 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:33:07.937374 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:33:07.979655 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:33:07.991869 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:33:08.034514 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:33:08.1234 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:33:19.58208 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:33:19.662787 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:33:19.744218 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:33:19.767834 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:33:19.834143 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:33:19.914376 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:33:19.919883 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:33:19.932023 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:33:20.033726 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:33:20.039691 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:33:20.091407 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:33:20.132185 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:33:20.144281 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:33:20.185578 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:33:20.262714 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:33:45.889945 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:33:54.937891 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:34:20.419362 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:34:30.776049 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:34:31.418054 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_linear.rds
2026-02-10 01:34:31.479633 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_linear.rds
2026-02-10 01:34:31.518303 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_logistic.rds
2026-02-10 01:34:31.587691 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_logistic.rds
2026-02-10 01:34:54.966823 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:35:00.414199 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:35:00.727232 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_linear.rds
2026-02-10 01:35:00.789367 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_linear.rds
2026-02-10 01:35:00.828028 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_logistic.rds
2026-02-10 01:35:00.897054 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_logistic.rds
2026-02-10 01:35:20.13922 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:35:26.63467 WARNING::Fitting problem for feature 124 returning NA
2026-02-10 01:35:26.941485 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_linear.rds
2026-02-10 01:35:27.004417 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_linear.rds
2026-02-10 01:35:27.043663 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_logistic.rds
2026-02-10 01:35:27.115165 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_logistic.rds
2026-02-10 01:35:45.330969 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:35:45.412563 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:35:45.490978 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:35:45.5146 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:35:45.551875 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:35:45.633199 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:35:45.63907 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:35:45.651822 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:35:45.75378 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:35:45.759858 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:35:45.813391 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:35:45.888736 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:35:45.901212 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:35:45.943727 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:35:46.01697 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:35:58.106973 WARNING::Fitting problem for feature 50 returning NA
2026-02-10 01:35:58.184459 WARNING::Fitting problem for feature 62 returning NA
2026-02-10 01:35:58.259045 WARNING::Fitting problem for feature 74 returning NA
2026-02-10 01:35:58.280962 WARNING::Fitting problem for feature 78 returning NA
2026-02-10 01:35:58.315706 WARNING::Fitting problem for feature 84 returning NA
2026-02-10 01:35:58.391701 WARNING::Fitting problem for feature 96 returning NA
2026-02-10 01:35:58.397061 WARNING::Fitting problem for feature 97 returning NA
2026-02-10 01:35:58.408876 WARNING::Fitting problem for feature 99 returning NA
2026-02-10 01:35:58.503472 WARNING::Fitting problem for feature 114 returning NA
2026-02-10 01:35:58.508885 WARNING::Fitting problem for feature 115 returning NA
2026-02-10 01:35:58.558199 WARNING::Fitting problem for feature 123 returning NA
2026-02-10 01:35:58.598609 WARNING::Fitting problem for feature 130 returning NA
2026-02-10 01:35:58.610384 WARNING::Fitting problem for feature 132 returning NA
2026-02-10 01:35:58.650328 WARNING::Fitting problem for feature 139 returning NA
2026-02-10 01:35:58.718644 WARNING::Fitting problem for feature 150 returning NA
2026-02-10 01:35:58.96165 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_linear.rds
2026-02-10 01:35:59.023243 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_linear.rds
2026-02-10 01:35:59.086106 WARNING::Deleting existing residuals file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/residuals_logistic.rds
2026-02-10 01:35:59.383715 WARNING::Deleting existing fitted file: /tmp/RtmpjArkVZ/file1bfe46603088a6/fits/fitted_logistic.rds
2026-02-10 01:36:20.063976 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-10 01:36:20.081268 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-10 01:36:20.093107 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-10 01:36:20.146433 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-10 01:36:20.163838 ERROR::Effect name not found in metadata: d
2026-02-10 01:36:20.175047 ERROR::No user formula provided
2026-02-10 01:36:20.206122 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-10 01:36:20.217646 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-10 01:36:23.135878 INFO::Writing function arguments to log file
2026-02-10 01:36:23.150281 INFO::Verifying options selected are valid
2026-02-10 01:36:25.589632 INFO::Writing function arguments to log file
2026-02-10 01:36:25.601757 INFO::Verifying options selected are valid
2026-02-10 01:36:25.60287 INFO::Determining format of input files
2026-02-10 01:36:25.603892 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-10 01:36:25.606248 INFO::Running selected normalization method: TSS
2026-02-10 01:36:25.60775 INFO::Creating output feature tables folder
2026-02-10 01:36:25.608701 INFO::Writing normalized data to file /tmp/RtmpjArkVZ/file1bfe465073798f/features/data_norm.tsv
2026-02-10 01:36:25.61016 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-10 01:36:25.61105 INFO::Total samples in data: 16
2026-02-10 01:36:25.611897 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-10 01:36:25.612741 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-10 01:36:25.614673 INFO::Total filtered features: 0
2026-02-10 01:36:25.615619 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-10 01:36:25.61676 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-10 01:36:25.617685 INFO::Filtered feature names from variance filtering:
2026-02-10 01:36:25.618549 INFO::Writing filtered data to file /tmp/RtmpjArkVZ/file1bfe465073798f/features/filtered_data.tsv
2026-02-10 01:36:25.620067 INFO::Running selected transform method: LOG
2026-02-10 01:36:25.621282 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjArkVZ/file1bfe465073798f/features/data_transformed.tsv
2026-02-10 01:36:25.622998 INFO::Applying z-score to standardize continuous metadata
2026-02-10 01:36:25.62775 INFO::Running the linear model component
2026-02-10 01:36:25.641482 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:25.646138 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:25.650498 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:25.65799 INFO::Counting total values for each feature
2026-02-10 01:36:25.659843 INFO::Running the logistic model component
2026-02-10 01:36:25.673611 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:25.680612 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:25.687387 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:25.697257 INFO::Counting total values for each feature
2026-02-10 01:36:25.699657 INFO::Re-running abundances for warn_prevalence
2026-02-10 01:36:25.700678 INFO::Running selected normalization method: TSS
2026-02-10 01:36:25.702208 INFO::Running selected transform method: LOG
2026-02-10 01:36:25.716204 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:25.720939 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:25.725368 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:25.806347 INFO::Creating fits folder
2026-02-10 01:36:25.807603 INFO::Writing residuals to file /tmp/RtmpjArkVZ/file1bfe465073798f/fits/residuals_linear.rds
2026-02-10 01:36:25.808807 INFO::Writing fitted values to file /tmp/RtmpjArkVZ/file1bfe465073798f/fits/fitted_linear.rds
2026-02-10 01:36:25.810054 INFO::Writing residuals to file /tmp/RtmpjArkVZ/file1bfe465073798f/fits/residuals_logistic.rds
2026-02-10 01:36:25.811244 INFO::Writing fitted values to file /tmp/RtmpjArkVZ/file1bfe465073798f/fits/fitted_logistic.rds
2026-02-10 01:36:25.813681 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpjArkVZ/file1bfe465073798f/all_results.tsv
2026-02-10 01:36:25.815367 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/RtmpjArkVZ/file1bfe465073798f/significant_results.tsv
2026-02-10 01:36:25.816712 INFO::Creating output figures folder
2026-02-10 01:36:25.818058 INFO::Writing summary plot of significant
results to file: /tmp/RtmpjArkVZ/file1bfe465073798f/figures/summary_plot.pdf
2026-02-10 01:36:27.435528 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpjArkVZ/file1bfe465073798f/figures
2026-02-10 01:36:27.437503 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-10 01:36:27.442691 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-10 01:36:28.004322 INFO::Writing summary plot of
significant results to file: /tmp/RtmpjArkVZ/file1bfe465073798f/figures/summary_plot.pdf
2026-02-10 01:36:29.744631 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpjArkVZ/file1bfe465073798f/figures
2026-02-10 01:36:29.746311 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-10 01:36:29.751483 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-10 01:36:30.288667 INFO::Running the linear model component
2026-02-10 01:36:30.297982 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:30.302595 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:30.306763 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:30.314252 INFO::Counting total values for each feature
2026-02-10 01:36:30.316026 INFO::Running the logistic model component
2026-02-10 01:36:30.324664 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:30.330896 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:30.337092 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:30.346305 INFO::Counting total values for each feature
2026-02-10 01:36:30.348375 INFO::Re-running abundances for warn_prevalence
2026-02-10 01:36:30.349175 INFO::Running selected normalization method: TSS
2026-02-10 01:36:30.35057 INFO::Running selected transform method: LOG
2026-02-10 01:36:30.359388 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:30.363522 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:30.367497 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:30.445535 INFO::Creating output folder
2026-02-10 01:36:30.44665 INFO::Creating output figures folder
2026-02-10 01:36:30.447963 INFO::Writing summary plot of significant
results to file: /tmp/RtmpjArkVZ/file1bfe469c4f76e/figures/summary_plot.pdf
2026-02-10 01:36:32.12798 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpjArkVZ/file1bfe469c4f76e/figures
2026-02-10 01:36:32.129973 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-10 01:36:32.135467 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-10 01:36:33.115502 INFO::Applying z-score to standardize continuous metadata
2026-02-10 01:36:33.12291 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-10 01:36:33.123867 INFO::Bypass z-score application to metadata
2026-02-10 01:36:33.12659 INFO::Bypass z-score application to metadata
2026-02-10 01:36:33.146079 INFO::Determining format of input files
2026-02-10 01:36:33.147047 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-10 01:36:33.147889 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-10 01:36:33.15521 INFO::Determining format of input files
2026-02-10 01:36:33.156192 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-10 01:36:33.15747 INFO::Input format is feature_specific_covariate samples as columns
2026-02-10 01:36:33.165569 INFO::Determining format of input files
2026-02-10 01:36:33.166467 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-10 01:36:33.167451 INFO::Input format is feature_specific_covariate samples as columns
2026-02-10 01:36:33.169092 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-10 01:36:33.169853 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-10 01:36:33.181107 INFO::Running selected transform method: LOG
2026-02-10 01:36:33.1822 INFO::Creating output feature tables folder
2026-02-10 01:36:33.183051 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjArkVZ/file1bfe4634c56c14/features/data_transformed.tsv
2026-02-10 01:36:33.186805 INFO::Running selected transform method: LOG
2026-02-10 01:36:33.187796 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjArkVZ/file1bfe4634c56c14/features/data_transformed.tsv
2026-02-10 01:36:33.191768 INFO::Running selected transform method: PLOG
2026-02-10 01:36:33.193325 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjArkVZ/file1bfe4634c56c14/features/data_transformed.tsv
2026-02-10 01:36:33.196133 INFO::Running selected transform method: NONE
2026-02-10 01:36:33.196851 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpjArkVZ/file1bfe4634c56c14/features/data_transformed.tsv
2026-02-10 01:36:33.204016 INFO::Running the linear model component
2026-02-10 01:36:33.21244 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:33.216594 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:33.220487 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:33.227315 INFO::Counting total values for each feature
2026-02-10 01:36:33.228904 INFO::Running the logistic model component
2026-02-10 01:36:33.237162 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:33.243548 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:33.249523 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:33.258323 INFO::Counting total values for each feature
2026-02-10 01:36:33.260333 INFO::Re-running abundances for warn_prevalence
2026-02-10 01:36:33.261142 INFO::Running selected normalization method: TSS
2026-02-10 01:36:33.262518 INFO::Running selected transform method: LOG
2026-02-10 01:36:33.271016 INFO::Fitting model to feature number 1, a
2026-02-10 01:36:33.275178 INFO::Fitting model to feature number 2, b
2026-02-10 01:36:33.27914 INFO::Fitting model to feature number 3, c
2026-02-10 01:36:33.358025 INFO::Creating output folder
2026-02-10 01:36:33.359059 INFO::Creating fits folder
2026-02-10 01:36:33.359946 INFO::Writing residuals to file /tmp/RtmpjArkVZ/file1bfe465b654631/fits/residuals_linear.rds
2026-02-10 01:36:33.360995 INFO::Writing fitted values to file /tmp/RtmpjArkVZ/file1bfe465b654631/fits/fitted_linear.rds
2026-02-10 01:36:33.362117 INFO::Writing residuals to file /tmp/RtmpjArkVZ/file1bfe465b654631/fits/residuals_logistic.rds
2026-02-10 01:36:33.36324 INFO::Writing fitted values to file /tmp/RtmpjArkVZ/file1bfe465b654631/fits/fitted_logistic.rds
2026-02-10 01:36:33.3656 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpjArkVZ/file1bfe465b654631/all_results.tsv
2026-02-10 01:36:33.36712 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/RtmpjArkVZ/file1bfe465b654631/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
361.250 7.579 368.829
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.859 | 0.507 | 21.367 | |
| maaslin_check_arguments | 0.145 | 0.002 | 0.148 | |
| maaslin_check_formula | 0.161 | 0.002 | 0.163 | |
| maaslin_compute_formula | 0.152 | 0.001 | 0.153 | |
| maaslin_contrast_test | 19.191 | 0.362 | 19.555 | |
| maaslin_filter | 0.450 | 0.030 | 0.481 | |
| maaslin_fit | 12.948 | 0.093 | 13.042 | |
| maaslin_log_arguments | 0.131 | 0.004 | 0.135 | |
| maaslin_normalize | 0.280 | 0.001 | 0.281 | |
| maaslin_plot_results | 43.462 | 0.330 | 43.759 | |
| maaslin_plot_results_from_output | 42.624 | 0.388 | 43.016 | |
| maaslin_process_metadata | 0.478 | 0.012 | 0.490 | |
| maaslin_read_data | 0.136 | 0.001 | 0.137 | |
| maaslin_reorder_data | 0.134 | 0.002 | 0.137 | |
| maaslin_transform | 0.557 | 0.013 | 0.570 | |
| maaslin_write_results | 14.009 | 0.239 | 14.249 | |
| maaslin_write_results_lefse_format | 14.100 | 0.053 | 14.155 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.013 | 0.000 | 0.013 | |