William Nickols
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-28 11:38 -0500 (Fri, 28 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 1155/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-28 02:35:59 -0500 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 02:50:22 -0500 (Fri, 28 Nov 2025) |
| EllapsedTime: 862.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 53.232 1.397 55.283
maaslin_plot_results 51.957 1.608 54.057
maaslin3 23.548 1.095 24.883
maaslin_contrast_test 21.843 1.181 23.211
maaslin_write_results_lefse_format 16.915 0.722 17.725
maaslin_write_results 15.605 0.763 16.464
maaslin_fit 14.738 0.623 15.461
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-28 02:43:24.785978 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:43:24.886569 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:43:25.026846 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:43:25.055329 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:43:25.107734 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:43:25.216939 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:43:25.238315 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:43:25.257922 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:43:25.389697 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:43:25.39797 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:43:25.472684 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:43:25.5459 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:43:25.564131 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:43:25.624132 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:43:25.722374 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:43:43.431771 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:43:43.535474 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:43:43.656476 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:43:43.684163 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:43:43.72899 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:43:43.839219 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:43:43.847895 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:43:43.864957 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:43:43.998391 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:43:44.005724 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:43:44.068825 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:43:44.125579 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:43:44.141379 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:43:44.194758 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:43:44.310371 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:43:49.044 R[15671:32235967] XType: Using static font registry.
2025-11-28 02:44:13.154374 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:44:13.245259 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:44:13.335353 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:44:13.364484 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:44:13.419228 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:44:13.552233 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:44:13.562085 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:44:13.583004 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:44:13.724422 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:44:13.733246 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:44:13.81842 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:44:13.886056 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:44:13.904033 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:44:13.960847 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:44:14.048549 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:44:29.911523 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:44:30.016372 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:44:30.109477 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:44:30.140674 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:44:30.179593 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:44:30.283125 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:44:30.290715 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:44:30.309193 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:44:30.461144 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:44:30.470171 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:44:30.542225 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:44:30.596697 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:44:30.615054 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:44:30.679457 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:44:30.791987 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:44:31.125808 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/residuals_linear.rds
2025-11-28 02:44:31.184546 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/fitted_linear.rds
2025-11-28 02:44:31.247168 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/residuals_logistic.rds
2025-11-28 02:44:31.576566 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/fitted_logistic.rds
2025-11-28 02:44:56.345911 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:44:56.455289 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:44:56.556405 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:44:56.583161 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:44:56.631106 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:44:56.722437 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:44:56.73169 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:44:56.75385 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:44:56.898235 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:44:56.906948 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:44:56.971052 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:44:57.026341 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:44:57.040468 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:44:57.094373 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:44:57.231125 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:45:11.543011 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:45:11.649804 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:45:11.751382 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:45:11.77916 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:45:11.825529 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:45:11.9226 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:45:11.929358 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:45:11.945231 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:45:12.06223 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:45:12.070134 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:45:12.132863 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:45:12.183318 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:45:12.200851 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:45:12.255979 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:45:12.351212 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:45:12.640171 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/residuals_linear.rds
2025-11-28 02:45:12.698442 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/fitted_linear.rds
2025-11-28 02:45:12.757044 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/residuals_logistic.rds
2025-11-28 02:45:13.062836 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/fitted_logistic.rds
2025-11-28 02:45:37.841052 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:45:37.941756 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:45:38.045586 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:45:38.074692 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:45:38.119557 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:45:38.218923 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:45:38.225347 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:45:38.269324 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:45:38.394828 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:45:38.403043 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:45:38.466134 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:45:38.51631 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:45:38.531798 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:45:38.583662 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:45:38.674421 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:45:52.376995 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:45:52.467695 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:45:52.555987 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:45:52.582915 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:45:52.628273 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:45:52.726219 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:45:52.734285 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:45:52.750312 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:45:52.872663 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:45:52.880487 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:45:52.946829 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:45:52.999633 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:45:53.013409 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:45:53.06529 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:45:53.140443 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:45:53.391659 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/residuals_linear.rds
2025-11-28 02:45:53.459135 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/fitted_linear.rds
2025-11-28 02:45:53.528025 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/residuals_logistic.rds
2025-11-28 02:45:53.847475 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3777ff59c5/fits/fitted_logistic.rds
2025-11-28 02:46:18.463816 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:46:18.562055 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:46:18.666605 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:46:18.68998 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:46:18.729435 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:46:18.828484 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:46:18.836566 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:46:18.850814 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:46:18.978248 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:46:18.986777 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:46:19.053459 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:46:19.11378 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:46:19.131127 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:46:19.180901 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:46:19.281054 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:46:32.937007 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:46:33.035011 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:46:33.129006 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:46:33.154464 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:46:33.202039 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:46:33.313515 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:46:33.321056 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:46:33.336837 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:46:33.465726 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:46:33.473676 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:46:33.530026 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:46:33.580219 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:46:33.597995 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:46:33.649289 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:46:33.738137 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:47:00.723414 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:47:11.536856 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:47:39.526649 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:47:50.865079 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:47:51.566112 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_linear.rds
2025-11-28 02:47:51.628295 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_linear.rds
2025-11-28 02:47:51.667372 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_logistic.rds
2025-11-28 02:47:51.743387 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_logistic.rds
2025-11-28 02:48:18.39688 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:48:25.930227 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:48:26.373148 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_linear.rds
2025-11-28 02:48:26.445274 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_linear.rds
2025-11-28 02:48:26.487439 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_logistic.rds
2025-11-28 02:48:26.564621 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_logistic.rds
2025-11-28 02:48:48.566975 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:48:55.797979 WARNING::Fitting problem for feature 124 returning NA
2025-11-28 02:48:56.153176 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_linear.rds
2025-11-28 02:48:56.215342 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_linear.rds
2025-11-28 02:48:56.258681 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_logistic.rds
2025-11-28 02:48:56.331039 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_logistic.rds
2025-11-28 02:49:17.560273 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:49:17.662005 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:49:17.758758 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:49:17.787698 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:49:17.836407 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:49:17.937119 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:49:17.944605 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:49:17.960822 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:49:18.08101 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:49:18.089953 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:49:18.194956 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:49:18.246296 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:49:18.262686 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:49:18.311044 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:49:18.404158 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:49:32.539079 WARNING::Fitting problem for feature 50 returning NA
2025-11-28 02:49:32.636767 WARNING::Fitting problem for feature 62 returning NA
2025-11-28 02:49:32.721534 WARNING::Fitting problem for feature 74 returning NA
2025-11-28 02:49:32.753757 WARNING::Fitting problem for feature 78 returning NA
2025-11-28 02:49:32.796788 WARNING::Fitting problem for feature 84 returning NA
2025-11-28 02:49:32.890039 WARNING::Fitting problem for feature 96 returning NA
2025-11-28 02:49:32.895428 WARNING::Fitting problem for feature 97 returning NA
2025-11-28 02:49:32.90858 WARNING::Fitting problem for feature 99 returning NA
2025-11-28 02:49:33.030286 WARNING::Fitting problem for feature 114 returning NA
2025-11-28 02:49:33.039267 WARNING::Fitting problem for feature 115 returning NA
2025-11-28 02:49:33.115924 WARNING::Fitting problem for feature 123 returning NA
2025-11-28 02:49:33.168807 WARNING::Fitting problem for feature 130 returning NA
2025-11-28 02:49:33.185786 WARNING::Fitting problem for feature 132 returning NA
2025-11-28 02:49:33.24189 WARNING::Fitting problem for feature 139 returning NA
2025-11-28 02:49:33.336351 WARNING::Fitting problem for feature 150 returning NA
2025-11-28 02:49:33.625801 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_linear.rds
2025-11-28 02:49:33.692534 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_linear.rds
2025-11-28 02:49:33.757908 WARNING::Deleting existing residuals file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/residuals_logistic.rds
2025-11-28 02:49:34.087796 WARNING::Deleting existing fitted file: /tmp/Rtmp2TN15f/file3d3747bd3250/fits/fitted_logistic.rds
2025-11-28 02:49:56.693071 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-28 02:49:56.710782 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-28 02:49:56.727255 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-28 02:49:56.794381 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-28 02:49:56.810618 ERROR::Effect name not found in metadata: d
2025-11-28 02:49:56.824944 ERROR::No user formula provided
2025-11-28 02:49:56.867233 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-28 02:49:56.880962 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-28 02:50:00.257631 INFO::Writing function arguments to log file
2025-11-28 02:50:00.278239 INFO::Verifying options selected are valid
2025-11-28 02:50:02.945004 INFO::Writing function arguments to log file
2025-11-28 02:50:02.963309 INFO::Verifying options selected are valid
2025-11-28 02:50:02.96472 INFO::Determining format of input files
2025-11-28 02:50:02.965996 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 02:50:02.968846 INFO::Running selected normalization method: TSS
2025-11-28 02:50:02.970414 INFO::Creating output feature tables folder
2025-11-28 02:50:02.972097 INFO::Writing normalized data to file /tmp/Rtmp2TN15f/file3d37556c4468/features/data_norm.tsv
2025-11-28 02:50:02.974061 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-28 02:50:02.975355 INFO::Total samples in data: 16
2025-11-28 02:50:02.976762 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-28 02:50:02.97779 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-28 02:50:02.980121 INFO::Total filtered features: 0
2025-11-28 02:50:02.98158 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-28 02:50:02.983106 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-28 02:50:02.984192 INFO::Filtered feature names from variance filtering:
2025-11-28 02:50:02.98549 INFO::Writing filtered data to file /tmp/Rtmp2TN15f/file3d37556c4468/features/filtered_data.tsv
2025-11-28 02:50:02.987631 INFO::Running selected transform method: LOG
2025-11-28 02:50:02.988988 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp2TN15f/file3d37556c4468/features/data_transformed.tsv
2025-11-28 02:50:02.991366 INFO::Applying z-score to standardize continuous metadata
2025-11-28 02:50:02.997821 INFO::Running the linear model component
2025-11-28 02:50:03.021266 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:03.027332 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:03.033682 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:03.043501 INFO::Counting total values for each feature
2025-11-28 02:50:03.045862 INFO::Running the logistic model component
2025-11-28 02:50:03.070994 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:03.07975 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:03.089745 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:03.101929 INFO::Counting total values for each feature
2025-11-28 02:50:03.105494 INFO::Re-running abundances for warn_prevalence
2025-11-28 02:50:03.107326 INFO::Running selected normalization method: TSS
2025-11-28 02:50:03.109972 INFO::Running selected transform method: LOG
2025-11-28 02:50:03.133533 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:03.14047 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:03.145884 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:03.259767 INFO::Creating fits folder
2025-11-28 02:50:03.261284 INFO::Writing residuals to file /tmp/Rtmp2TN15f/file3d37556c4468/fits/residuals_linear.rds
2025-11-28 02:50:03.262727 INFO::Writing fitted values to file /tmp/Rtmp2TN15f/file3d37556c4468/fits/fitted_linear.rds
2025-11-28 02:50:03.264171 INFO::Writing residuals to file /tmp/Rtmp2TN15f/file3d37556c4468/fits/residuals_logistic.rds
2025-11-28 02:50:03.265591 INFO::Writing fitted values to file /tmp/Rtmp2TN15f/file3d37556c4468/fits/fitted_logistic.rds
2025-11-28 02:50:03.269231 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp2TN15f/file3d37556c4468/all_results.tsv
2025-11-28 02:50:03.272186 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/Rtmp2TN15f/file3d37556c4468/significant_results.tsv
2025-11-28 02:50:03.27472 INFO::Creating output figures folder
2025-11-28 02:50:03.277091 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp2TN15f/file3d37556c4468/figures/summary_plot.pdf
2025-11-28 02:50:05.33923 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp2TN15f/file3d37556c4468/figures
2025-11-28 02:50:05.341773 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 02:50:05.348491 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 02:50:05.979248 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp2TN15f/file3d37556c4468/figures/summary_plot.pdf
2025-11-28 02:50:07.864909 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp2TN15f/file3d37556c4468/figures
2025-11-28 02:50:07.866336 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 02:50:07.872506 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 02:50:08.470386 INFO::Running the linear model component
2025-11-28 02:50:08.4819 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:08.487371 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:08.491523 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:08.500032 INFO::Counting total values for each feature
2025-11-28 02:50:08.502596 INFO::Running the logistic model component
2025-11-28 02:50:08.514724 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:08.522918 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:08.530342 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:08.543565 INFO::Counting total values for each feature
2025-11-28 02:50:08.546721 INFO::Re-running abundances for warn_prevalence
2025-11-28 02:50:08.548062 INFO::Running selected normalization method: TSS
2025-11-28 02:50:08.550134 INFO::Running selected transform method: LOG
2025-11-28 02:50:08.558553 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:08.563504 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:08.569044 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:08.67826 INFO::Creating output folder
2025-11-28 02:50:08.679695 INFO::Creating output figures folder
2025-11-28 02:50:08.681109 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp2TN15f/file3d374d9fa39a/figures/summary_plot.pdf
2025-11-28 02:50:10.654677 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp2TN15f/file3d374d9fa39a/figures
2025-11-28 02:50:10.656883 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-28 02:50:10.664862 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-28 02:50:11.898692 INFO::Applying z-score to standardize continuous metadata
2025-11-28 02:50:11.907525 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-28 02:50:11.90834 INFO::Bypass z-score application to metadata
2025-11-28 02:50:11.911092 INFO::Bypass z-score application to metadata
2025-11-28 02:50:11.941223 INFO::Determining format of input files
2025-11-28 02:50:11.942667 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 02:50:11.94396 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-28 02:50:11.952709 INFO::Determining format of input files
2025-11-28 02:50:11.95384 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-28 02:50:11.955088 INFO::Input format is feature_specific_covariate samples as columns
2025-11-28 02:50:11.963574 INFO::Determining format of input files
2025-11-28 02:50:11.964542 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-28 02:50:11.965513 INFO::Input format is feature_specific_covariate samples as columns
2025-11-28 02:50:11.966934 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-28 02:50:11.96761 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-28 02:50:11.982435 INFO::Running selected transform method: LOG
2025-11-28 02:50:11.98364 INFO::Creating output feature tables folder
2025-11-28 02:50:11.9847 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp2TN15f/file3d377bfa434b/features/data_transformed.tsv
2025-11-28 02:50:11.990352 INFO::Running selected transform method: LOG
2025-11-28 02:50:11.99203 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp2TN15f/file3d377bfa434b/features/data_transformed.tsv
2025-11-28 02:50:11.997975 INFO::Running selected transform method: PLOG
2025-11-28 02:50:12.000547 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp2TN15f/file3d377bfa434b/features/data_transformed.tsv
2025-11-28 02:50:12.004267 INFO::Running selected transform method: NONE
2025-11-28 02:50:12.005077 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp2TN15f/file3d377bfa434b/features/data_transformed.tsv
2025-11-28 02:50:12.016631 INFO::Running the linear model component
2025-11-28 02:50:12.026328 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:12.032621 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:12.037413 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:12.044107 INFO::Counting total values for each feature
2025-11-28 02:50:12.045704 INFO::Running the logistic model component
2025-11-28 02:50:12.057218 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:12.064587 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:12.071563 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:12.102838 INFO::Counting total values for each feature
2025-11-28 02:50:12.105256 INFO::Re-running abundances for warn_prevalence
2025-11-28 02:50:12.10632 INFO::Running selected normalization method: TSS
2025-11-28 02:50:12.107892 INFO::Running selected transform method: LOG
2025-11-28 02:50:12.120145 INFO::Fitting model to feature number 1, a
2025-11-28 02:50:12.125335 INFO::Fitting model to feature number 2, b
2025-11-28 02:50:12.129929 INFO::Fitting model to feature number 3, c
2025-11-28 02:50:12.230495 INFO::Creating output folder
2025-11-28 02:50:12.231614 INFO::Creating fits folder
2025-11-28 02:50:12.232573 INFO::Writing residuals to file /tmp/Rtmp2TN15f/file3d376b583083/fits/residuals_linear.rds
2025-11-28 02:50:12.233716 INFO::Writing fitted values to file /tmp/Rtmp2TN15f/file3d376b583083/fits/fitted_linear.rds
2025-11-28 02:50:12.23477 INFO::Writing residuals to file /tmp/Rtmp2TN15f/file3d376b583083/fits/residuals_logistic.rds
2025-11-28 02:50:12.235824 INFO::Writing fitted values to file /tmp/Rtmp2TN15f/file3d376b583083/fits/fitted_logistic.rds
2025-11-28 02:50:12.238273 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp2TN15f/file3d376b583083/all_results.tsv
2025-11-28 02:50:12.240649 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/Rtmp2TN15f/file3d376b583083/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
409.898 8.041 420.772
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 23.548 | 1.095 | 24.883 | |
| maaslin_check_arguments | 0.194 | 0.005 | 0.201 | |
| maaslin_check_formula | 0.176 | 0.011 | 0.189 | |
| maaslin_compute_formula | 0.185 | 0.012 | 0.200 | |
| maaslin_contrast_test | 21.843 | 1.181 | 23.211 | |
| maaslin_filter | 0.625 | 0.046 | 0.677 | |
| maaslin_fit | 14.738 | 0.623 | 15.461 | |
| maaslin_log_arguments | 0.175 | 0.009 | 0.185 | |
| maaslin_normalize | 0.390 | 0.034 | 0.429 | |
| maaslin_plot_results | 51.957 | 1.608 | 54.057 | |
| maaslin_plot_results_from_output | 53.232 | 1.397 | 55.283 | |
| maaslin_process_metadata | 0.659 | 0.043 | 0.712 | |
| maaslin_read_data | 0.175 | 0.011 | 0.187 | |
| maaslin_reorder_data | 0.205 | 0.024 | 0.231 | |
| maaslin_transform | 0.797 | 0.056 | 0.865 | |
| maaslin_write_results | 15.605 | 0.763 | 16.464 | |
| maaslin_write_results_lefse_format | 16.915 | 0.722 | 17.725 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.005 | |