William Nickols
| Snapshot Date: 2026-02-26 13:45 -0500 (Thu, 26 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 2026-02-27 11:57 -0500 (Fri, 27 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: 2026-02-27 00:58:48 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 01:20:27 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 1299.3 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 43.329 0.428 43.726
maaslin_plot_results_from_output 42.545 0.426 42.974
maaslin3 19.554 0.811 20.366
maaslin_contrast_test 18.661 0.560 19.223
maaslin_write_results_lefse_format 14.640 0.086 14.727
maaslin_write_results 14.074 0.175 14.251
maaslin_fit 12.617 0.104 12.722
* 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")
2026-02-27 01:05:01.140062 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:05:01.225041 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:05:01.316169 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:05:01.337258 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:05:01.371907 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:05:01.447934 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:05:01.461586 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:05:01.473558 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:05:01.568825 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:05:01.574351 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:05:01.624242 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:05:01.675114 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:05:01.687255 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:05:01.727577 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:05:01.796895 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:05:17.546022 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:05:17.6199 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:05:17.692019 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:05:17.713177 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:05:17.746324 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:05:17.833895 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:05:17.839308 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:05:17.851406 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:05:17.94359 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:05:17.948932 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:05:17.996923 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:05:18.035358 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:05:18.046739 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:05:18.085736 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:05:18.153672 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:05:42.365452 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:05:42.440753 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:05:42.516147 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:05:42.5384 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:05:42.572778 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:05:42.646558 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:05:42.651865 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:05:42.664132 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:05:42.7592 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:05:42.764628 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:05:42.816494 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:05:42.858415 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:05:42.871391 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:05:42.913157 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:05:42.98383 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:05:55.739059 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:05:55.839787 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:05:55.912977 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:05:55.93434 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:05:55.96855 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:05:56.043164 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:05:56.048447 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:05:56.060167 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:05:56.153969 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:05:56.159711 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:05:56.210139 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:05:56.250376 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:05:56.262024 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:05:56.301199 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:05:56.368277 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:05:56.568038 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/residuals_linear.rds
2026-02-27 01:05:56.629875 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/fitted_linear.rds
2026-02-27 01:05:56.693674 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/residuals_logistic.rds
2026-02-27 01:05:56.993793 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/fitted_logistic.rds
2026-02-27 01:06:19.137033 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:06:19.212362 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:06:19.311403 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:06:19.332855 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:06:19.366669 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:06:19.441618 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:06:19.446846 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:06:19.458334 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:06:19.55067 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:06:19.555988 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:06:19.60428 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:06:19.643202 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:06:19.654815 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:06:19.693839 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:06:19.760748 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:06:31.697873 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:06:31.780936 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:06:31.858808 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:06:31.882143 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:06:31.918836 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:06:31.997575 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:06:32.002984 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:06:32.014915 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:06:32.111482 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:06:32.116956 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:06:32.167278 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:06:32.207677 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:06:32.219809 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:06:32.261417 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:06:32.332045 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:06:32.535881 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/residuals_linear.rds
2026-02-27 01:06:32.596747 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/fitted_linear.rds
2026-02-27 01:06:32.659729 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/residuals_logistic.rds
2026-02-27 01:06:32.959995 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/fitted_logistic.rds
2026-02-27 01:06:54.06511 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:06:54.145644 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:06:54.225607 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:06:54.250577 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:06:54.287892 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:06:54.395326 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:06:54.400821 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:06:54.413063 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:06:54.51215 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:06:54.51771 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:06:54.568869 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:06:54.610178 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:06:54.623038 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:06:54.666147 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:06:54.735317 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:07:06.549867 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:07:06.627758 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:07:06.705761 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:07:06.728802 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:07:06.764031 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:07:06.83854 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:07:06.843801 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:07:06.855429 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:07:06.952569 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:07:06.958651 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:07:07.009596 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:07:07.050788 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:07:07.062916 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:07:07.104544 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:07:07.176459 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:07:07.379804 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/residuals_linear.rds
2026-02-27 01:07:07.440617 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/fitted_linear.rds
2026-02-27 01:07:07.503799 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/residuals_logistic.rds
2026-02-27 01:07:07.803826 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd3bf9a817/fits/fitted_logistic.rds
2026-02-27 01:07:29.041181 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:07:29.117324 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:07:29.193075 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:07:29.215189 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:07:29.250707 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:07:29.326867 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:07:29.332488 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:07:29.344574 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:07:29.439903 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:07:29.445267 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:07:29.495231 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:07:29.535623 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:07:29.547665 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:07:29.588451 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:07:29.657827 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:07:41.304718 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:07:41.378913 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:07:41.451755 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:07:41.473094 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:07:41.507165 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:07:41.582517 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:07:41.587796 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:07:41.599382 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:07:41.692993 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:07:41.698292 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:07:41.74691 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:07:41.788027 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:07:41.80024 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:07:41.840849 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:07:41.909366 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:08:07.115444 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:08:15.921427 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:08:40.97171 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:08:51.118752 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:08:51.756702 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_linear.rds
2026-02-27 01:08:51.818726 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_linear.rds
2026-02-27 01:08:51.857761 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_logistic.rds
2026-02-27 01:08:51.926841 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_logistic.rds
2026-02-27 01:09:15.253924 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:09:20.526047 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:09:20.835197 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_linear.rds
2026-02-27 01:09:20.896876 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_linear.rds
2026-02-27 01:09:20.935345 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_logistic.rds
2026-02-27 01:09:21.004096 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_logistic.rds
2026-02-27 01:09:40.236154 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:09:46.74676 WARNING::Fitting problem for feature 124 returning NA
2026-02-27 01:09:47.048417 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_linear.rds
2026-02-27 01:09:47.109856 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_linear.rds
2026-02-27 01:09:47.148517 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_logistic.rds
2026-02-27 01:09:47.217873 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_logistic.rds
2026-02-27 01:10:05.70026 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:10:05.779592 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:10:05.857439 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:10:05.880548 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:10:05.915437 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:10:05.993588 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:10:05.999207 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:10:06.011824 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:10:06.109924 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:10:06.115538 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:10:06.165386 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:10:06.205754 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:10:06.218074 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:10:06.25911 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:10:06.328684 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:10:18.444545 WARNING::Fitting problem for feature 50 returning NA
2026-02-27 01:10:18.526089 WARNING::Fitting problem for feature 62 returning NA
2026-02-27 01:10:18.606194 WARNING::Fitting problem for feature 74 returning NA
2026-02-27 01:10:18.628663 WARNING::Fitting problem for feature 78 returning NA
2026-02-27 01:10:18.664008 WARNING::Fitting problem for feature 84 returning NA
2026-02-27 01:10:18.743451 WARNING::Fitting problem for feature 96 returning NA
2026-02-27 01:10:18.749656 WARNING::Fitting problem for feature 97 returning NA
2026-02-27 01:10:18.762233 WARNING::Fitting problem for feature 99 returning NA
2026-02-27 01:10:18.893653 WARNING::Fitting problem for feature 114 returning NA
2026-02-27 01:10:18.899956 WARNING::Fitting problem for feature 115 returning NA
2026-02-27 01:10:18.954239 WARNING::Fitting problem for feature 123 returning NA
2026-02-27 01:10:18.997209 WARNING::Fitting problem for feature 130 returning NA
2026-02-27 01:10:19.010003 WARNING::Fitting problem for feature 132 returning NA
2026-02-27 01:10:19.052573 WARNING::Fitting problem for feature 139 returning NA
2026-02-27 01:10:19.123019 WARNING::Fitting problem for feature 150 returning NA
2026-02-27 01:10:19.366707 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_linear.rds
2026-02-27 01:10:19.427656 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_linear.rds
2026-02-27 01:10:19.490662 WARNING::Deleting existing residuals file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/residuals_logistic.rds
2026-02-27 01:10:19.789681 WARNING::Deleting existing fitted file: /tmp/RtmpTNvWLx/file2481fd509560b2/fits/fitted_logistic.rds
2026-02-27 01:10:40.275821 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-27 01:10:40.29341 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-27 01:10:40.305443 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-27 01:10:40.360569 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-27 01:10:40.377931 ERROR::Effect name not found in metadata: d
2026-02-27 01:10:40.389714 ERROR::No user formula provided
2026-02-27 01:10:40.422433 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-27 01:10:40.435125 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-27 01:10:43.269499 INFO::Writing function arguments to log file
2026-02-27 01:10:43.283977 INFO::Verifying options selected are valid
2026-02-27 01:10:45.590494 INFO::Writing function arguments to log file
2026-02-27 01:10:45.6029 INFO::Verifying options selected are valid
2026-02-27 01:10:45.604022 INFO::Determining format of input files
2026-02-27 01:10:45.605051 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-27 01:10:45.607486 INFO::Running selected normalization method: TSS
2026-02-27 01:10:45.609063 INFO::Creating output feature tables folder
2026-02-27 01:10:45.610106 INFO::Writing normalized data to file /tmp/RtmpTNvWLx/file2481fd65388e73/features/data_norm.tsv
2026-02-27 01:10:45.611696 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-27 01:10:45.612661 INFO::Total samples in data: 16
2026-02-27 01:10:45.613569 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-27 01:10:45.614464 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-27 01:10:45.61646 INFO::Total filtered features: 0
2026-02-27 01:10:45.617446 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-27 01:10:45.61864 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-27 01:10:45.619613 INFO::Filtered feature names from variance filtering:
2026-02-27 01:10:45.620516 INFO::Writing filtered data to file /tmp/RtmpTNvWLx/file2481fd65388e73/features/filtered_data.tsv
2026-02-27 01:10:45.622044 INFO::Running selected transform method: LOG
2026-02-27 01:10:45.623277 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTNvWLx/file2481fd65388e73/features/data_transformed.tsv
2026-02-27 01:10:45.624979 INFO::Applying z-score to standardize continuous metadata
2026-02-27 01:10:45.629591 INFO::Running the linear model component
2026-02-27 01:10:45.643835 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:45.64861 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:45.653065 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:45.660539 INFO::Counting total values for each feature
2026-02-27 01:10:45.662532 INFO::Running the logistic model component
2026-02-27 01:10:45.676636 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:45.683167 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:45.689343 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:45.69829 INFO::Counting total values for each feature
2026-02-27 01:10:45.700501 INFO::Re-running abundances for warn_prevalence
2026-02-27 01:10:45.701459 INFO::Running selected normalization method: TSS
2026-02-27 01:10:45.702955 INFO::Running selected transform method: LOG
2026-02-27 01:10:45.716949 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:45.721439 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:45.72566 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:45.836593 INFO::Creating fits folder
2026-02-27 01:10:45.837864 INFO::Writing residuals to file /tmp/RtmpTNvWLx/file2481fd65388e73/fits/residuals_linear.rds
2026-02-27 01:10:45.839052 INFO::Writing fitted values to file /tmp/RtmpTNvWLx/file2481fd65388e73/fits/fitted_linear.rds
2026-02-27 01:10:45.84026 INFO::Writing residuals to file /tmp/RtmpTNvWLx/file2481fd65388e73/fits/residuals_logistic.rds
2026-02-27 01:10:45.841465 INFO::Writing fitted values to file /tmp/RtmpTNvWLx/file2481fd65388e73/fits/fitted_logistic.rds
2026-02-27 01:10:45.843929 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpTNvWLx/file2481fd65388e73/all_results.tsv
2026-02-27 01:10:45.845703 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/RtmpTNvWLx/file2481fd65388e73/significant_results.tsv
2026-02-27 01:10:45.847081 INFO::Creating output figures folder
2026-02-27 01:10:45.848496 INFO::Writing summary plot of significant
results to file: /tmp/RtmpTNvWLx/file2481fd65388e73/figures/summary_plot.pdf
2026-02-27 01:10:47.472697 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTNvWLx/file2481fd65388e73/figures
2026-02-27 01:10:47.474639 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-27 01:10:47.47976 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-27 01:10:48.009029 INFO::Writing summary plot of
significant results to file: /tmp/RtmpTNvWLx/file2481fd65388e73/figures/summary_plot.pdf
2026-02-27 01:10:49.63882 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTNvWLx/file2481fd65388e73/figures
2026-02-27 01:10:49.640402 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-27 01:10:49.645328 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-27 01:10:50.166939 INFO::Running the linear model component
2026-02-27 01:10:50.175987 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:50.180543 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:50.184688 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:50.191684 INFO::Counting total values for each feature
2026-02-27 01:10:50.19337 INFO::Running the logistic model component
2026-02-27 01:10:50.201682 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:50.208127 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:50.214249 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:50.223189 INFO::Counting total values for each feature
2026-02-27 01:10:50.22525 INFO::Re-running abundances for warn_prevalence
2026-02-27 01:10:50.226069 INFO::Running selected normalization method: TSS
2026-02-27 01:10:50.227417 INFO::Running selected transform method: LOG
2026-02-27 01:10:50.235938 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:50.24024 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:50.244351 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:50.323559 INFO::Creating output folder
2026-02-27 01:10:50.324556 INFO::Creating output figures folder
2026-02-27 01:10:50.325848 INFO::Writing summary plot of significant
results to file: /tmp/RtmpTNvWLx/file2481fd7a6f6588/figures/summary_plot.pdf
2026-02-27 01:10:51.99226 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpTNvWLx/file2481fd7a6f6588/figures
2026-02-27 01:10:51.994119 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-27 01:10:51.999696 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-27 01:10:52.981203 INFO::Applying z-score to standardize continuous metadata
2026-02-27 01:10:52.988354 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-27 01:10:52.989248 INFO::Bypass z-score application to metadata
2026-02-27 01:10:52.991857 INFO::Bypass z-score application to metadata
2026-02-27 01:10:53.022777 INFO::Determining format of input files
2026-02-27 01:10:53.024093 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-27 01:10:53.025171 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-27 01:10:53.033179 INFO::Determining format of input files
2026-02-27 01:10:53.034173 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-27 01:10:53.03546 INFO::Input format is feature_specific_covariate samples as columns
2026-02-27 01:10:53.043594 INFO::Determining format of input files
2026-02-27 01:10:53.044521 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-27 01:10:53.045554 INFO::Input format is feature_specific_covariate samples as columns
2026-02-27 01:10:53.047233 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-27 01:10:53.048022 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-27 01:10:53.059434 INFO::Running selected transform method: LOG
2026-02-27 01:10:53.060581 INFO::Creating output feature tables folder
2026-02-27 01:10:53.061408 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTNvWLx/file2481fd4db21c9c/features/data_transformed.tsv
2026-02-27 01:10:53.065286 INFO::Running selected transform method: LOG
2026-02-27 01:10:53.066294 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTNvWLx/file2481fd4db21c9c/features/data_transformed.tsv
2026-02-27 01:10:53.070359 INFO::Running selected transform method: PLOG
2026-02-27 01:10:53.071903 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTNvWLx/file2481fd4db21c9c/features/data_transformed.tsv
2026-02-27 01:10:53.074859 INFO::Running selected transform method: NONE
2026-02-27 01:10:53.075618 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpTNvWLx/file2481fd4db21c9c/features/data_transformed.tsv
2026-02-27 01:10:53.083225 INFO::Running the linear model component
2026-02-27 01:10:53.091725 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:53.095997 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:53.100027 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:53.106919 INFO::Counting total values for each feature
2026-02-27 01:10:53.108571 INFO::Running the logistic model component
2026-02-27 01:10:53.116879 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:53.12313 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:53.129055 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:53.137891 INFO::Counting total values for each feature
2026-02-27 01:10:53.139937 INFO::Re-running abundances for warn_prevalence
2026-02-27 01:10:53.140745 INFO::Running selected normalization method: TSS
2026-02-27 01:10:53.14209 INFO::Running selected transform method: LOG
2026-02-27 01:10:53.150551 INFO::Fitting model to feature number 1, a
2026-02-27 01:10:53.154767 INFO::Fitting model to feature number 2, b
2026-02-27 01:10:53.158794 INFO::Fitting model to feature number 3, c
2026-02-27 01:10:53.235439 INFO::Creating output folder
2026-02-27 01:10:53.236421 INFO::Creating fits folder
2026-02-27 01:10:53.237256 INFO::Writing residuals to file /tmp/RtmpTNvWLx/file2481fd55040a61/fits/residuals_linear.rds
2026-02-27 01:10:53.238241 INFO::Writing fitted values to file /tmp/RtmpTNvWLx/file2481fd55040a61/fits/fitted_linear.rds
2026-02-27 01:10:53.239297 INFO::Writing residuals to file /tmp/RtmpTNvWLx/file2481fd55040a61/fits/residuals_logistic.rds
2026-02-27 01:10:53.240326 INFO::Writing fitted values to file /tmp/RtmpTNvWLx/file2481fd55040a61/fits/fitted_logistic.rds
2026-02-27 01:10:53.242596 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpTNvWLx/file2481fd55040a61/all_results.tsv
2026-02-27 01:10:53.244072 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/RtmpTNvWLx/file2481fd55040a61/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
358.468 4.613 363.063
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.554 | 0.811 | 20.366 | |
| maaslin_check_arguments | 0.139 | 0.001 | 0.140 | |
| maaslin_check_formula | 0.158 | 0.001 | 0.158 | |
| maaslin_compute_formula | 0.148 | 0.000 | 0.148 | |
| maaslin_contrast_test | 18.661 | 0.560 | 19.223 | |
| maaslin_filter | 0.441 | 0.038 | 0.479 | |
| maaslin_fit | 12.617 | 0.104 | 12.722 | |
| maaslin_log_arguments | 0.130 | 0.002 | 0.132 | |
| maaslin_normalize | 0.262 | 0.001 | 0.263 | |
| maaslin_plot_results | 43.329 | 0.428 | 43.726 | |
| maaslin_plot_results_from_output | 42.545 | 0.426 | 42.974 | |
| maaslin_process_metadata | 0.475 | 0.021 | 0.496 | |
| maaslin_read_data | 0.135 | 0.002 | 0.137 | |
| maaslin_reorder_data | 0.136 | 0.004 | 0.139 | |
| maaslin_transform | 0.569 | 0.015 | 0.583 | |
| maaslin_write_results | 14.074 | 0.175 | 14.251 | |
| maaslin_write_results_lefse_format | 14.640 | 0.086 | 14.727 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.003 | 0.000 | 0.004 | |