William Nickols
| Snapshot Date: 2026-02-19 13:45 -0500 (Thu, 19 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 2026-02-20 11:57 -0500 (Fri, 20 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" | 4890 |
| 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: 2026-02-20 01:44:16 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 02:06:04 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 1307.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 43.613 0.284 43.902
maaslin_plot_results 43.480 0.170 43.616
maaslin3 19.851 0.481 20.335
maaslin_contrast_test 19.089 0.469 19.561
maaslin_write_results_lefse_format 15.296 0.148 15.445
maaslin_write_results 13.545 0.118 13.665
maaslin_fit 13.409 0.112 13.524
* 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")
2026-02-20 01:50:35.111284 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:50:35.200029 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:50:35.297209 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:50:35.319633 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:50:35.354722 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:50:35.430638 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:50:35.442806 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:50:35.454484 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:50:35.550216 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:50:35.555603 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:50:35.605232 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:50:35.653247 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:50:35.664932 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:50:35.704634 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:50:35.774523 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:50:51.752532 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:50:51.827746 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:50:51.902182 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:50:51.924063 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:50:51.95803 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:50:52.050163 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:50:52.055763 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:50:52.067865 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:50:52.164235 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:50:52.169483 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:50:52.218903 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:50:52.259045 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:50:52.271089 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:50:52.312872 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:50:52.381736 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:51:17.032516 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:51:17.113052 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:51:17.198853 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:51:17.223279 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:51:17.258397 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:51:17.338425 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:51:17.344375 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:51:17.357056 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:51:17.459755 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:51:17.465438 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:51:17.518657 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:51:17.562231 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:51:17.575969 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:51:17.619475 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:51:17.692636 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:51:31.107784 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:51:31.217088 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:51:31.296135 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:51:31.319649 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:51:31.355299 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:51:31.433912 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:51:31.439529 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:51:31.452111 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:51:31.552238 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:51:31.558021 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:51:31.610357 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:51:31.651572 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:51:31.663692 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:51:31.704926 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:51:31.774256 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:51:31.979668 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/residuals_linear.rds
2026-02-20 01:51:32.04079 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/fitted_linear.rds
2026-02-20 01:51:32.104266 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/residuals_logistic.rds
2026-02-20 01:51:32.406096 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/fitted_logistic.rds
2026-02-20 01:51:54.924566 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:51:55.005676 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:51:55.114621 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:51:55.138261 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:51:55.1754 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:51:55.254685 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:51:55.260439 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:51:55.273026 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:51:55.39473 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:51:55.400909 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:51:55.454849 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:51:55.498555 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:51:55.511449 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:51:55.557171 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:51:55.633162 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:52:07.550494 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:52:07.631809 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:52:07.707597 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:52:07.72923 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:52:07.763319 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:52:07.837503 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:52:07.842873 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:52:07.854538 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:52:07.949719 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:52:07.955221 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:52:08.006293 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:52:08.046471 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:52:08.058475 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:52:08.100692 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:52:08.174351 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:52:08.383936 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/residuals_linear.rds
2026-02-20 01:52:08.445936 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/fitted_linear.rds
2026-02-20 01:52:08.509644 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/residuals_logistic.rds
2026-02-20 01:52:08.809102 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/fitted_logistic.rds
2026-02-20 01:52:30.378696 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:52:30.460216 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:52:30.541867 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:52:30.566361 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:52:30.606309 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:52:30.71427 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:52:30.720037 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:52:30.732983 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:52:30.833469 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:52:30.839041 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:52:30.88984 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:52:30.93055 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:52:30.94287 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:52:30.984573 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:52:31.054378 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:52:43.235551 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:52:43.314185 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:52:43.395058 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:52:43.417452 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:52:43.455161 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:52:43.536049 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:52:43.541882 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:52:43.55421 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:52:43.65445 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:52:43.660149 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:52:43.712428 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:52:43.755621 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:52:43.768737 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:52:43.814184 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:52:43.887356 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:52:44.109843 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/residuals_linear.rds
2026-02-20 01:52:44.171 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/fitted_linear.rds
2026-02-20 01:52:44.233949 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/residuals_logistic.rds
2026-02-20 01:52:44.535035 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c313a241371/fits/fitted_logistic.rds
2026-02-20 01:53:06.079114 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:53:06.157356 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:53:06.23693 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:53:06.25946 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:53:06.294392 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:53:06.371983 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:53:06.377799 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:53:06.389986 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:53:06.491867 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:53:06.498442 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:53:06.551772 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:53:06.592273 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:53:06.604244 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:53:06.645 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:53:06.714458 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:53:18.302201 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:53:18.380142 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:53:18.460358 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:53:18.483269 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:53:18.518103 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:53:18.595467 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:53:18.601019 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:53:18.613264 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:53:18.713794 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:53:18.719457 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:53:18.770996 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:53:18.815733 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:53:18.828649 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:53:18.871093 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:53:18.942826 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:53:45.159662 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:53:54.001986 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:54:19.280681 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:54:29.451402 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:54:30.064445 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_linear.rds
2026-02-20 01:54:30.126784 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_linear.rds
2026-02-20 01:54:30.166291 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_logistic.rds
2026-02-20 01:54:30.235343 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_logistic.rds
2026-02-20 01:54:53.05538 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:54:58.324403 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:54:58.622795 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_linear.rds
2026-02-20 01:54:58.684376 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_linear.rds
2026-02-20 01:54:58.723154 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_logistic.rds
2026-02-20 01:54:58.792783 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_logistic.rds
2026-02-20 01:55:17.931345 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:55:24.325232 WARNING::Fitting problem for feature 124 returning NA
2026-02-20 01:55:24.620553 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_linear.rds
2026-02-20 01:55:24.682179 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_linear.rds
2026-02-20 01:55:24.720808 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_logistic.rds
2026-02-20 01:55:24.790074 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_logistic.rds
2026-02-20 01:55:43.962409 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:55:44.037238 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:55:44.111874 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:55:44.133975 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:55:44.16867 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:55:44.244673 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:55:44.250211 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:55:44.262069 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:55:44.356814 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:55:44.362198 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:55:44.43722 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:55:44.477853 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:55:44.489882 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:55:44.53217 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:55:44.603844 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:55:55.408659 WARNING::Fitting problem for feature 50 returning NA
2026-02-20 01:55:55.484767 WARNING::Fitting problem for feature 62 returning NA
2026-02-20 01:55:55.559159 WARNING::Fitting problem for feature 74 returning NA
2026-02-20 01:55:55.580659 WARNING::Fitting problem for feature 78 returning NA
2026-02-20 01:55:55.614682 WARNING::Fitting problem for feature 84 returning NA
2026-02-20 01:55:55.691135 WARNING::Fitting problem for feature 96 returning NA
2026-02-20 01:55:55.696557 WARNING::Fitting problem for feature 97 returning NA
2026-02-20 01:55:55.70835 WARNING::Fitting problem for feature 99 returning NA
2026-02-20 01:55:55.803401 WARNING::Fitting problem for feature 114 returning NA
2026-02-20 01:55:55.809054 WARNING::Fitting problem for feature 115 returning NA
2026-02-20 01:55:55.861227 WARNING::Fitting problem for feature 123 returning NA
2026-02-20 01:55:55.902196 WARNING::Fitting problem for feature 130 returning NA
2026-02-20 01:55:55.914448 WARNING::Fitting problem for feature 132 returning NA
2026-02-20 01:55:55.954686 WARNING::Fitting problem for feature 139 returning NA
2026-02-20 01:55:56.028934 WARNING::Fitting problem for feature 150 returning NA
2026-02-20 01:55:56.315456 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_linear.rds
2026-02-20 01:55:56.376806 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_linear.rds
2026-02-20 01:55:56.439953 WARNING::Deleting existing residuals file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/residuals_logistic.rds
2026-02-20 01:55:56.739023 WARNING::Deleting existing fitted file: /tmp/RtmpQeV9fY/file1b2c3169a0ca91/fits/fitted_logistic.rds
2026-02-20 01:56:17.540177 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-20 01:56:17.55807 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-20 01:56:17.570325 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-20 01:56:17.625869 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-20 01:56:17.64449 ERROR::Effect name not found in metadata: d
2026-02-20 01:56:17.657655 ERROR::No user formula provided
2026-02-20 01:56:17.695031 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-20 01:56:17.708548 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-20 01:56:20.584517 INFO::Writing function arguments to log file
2026-02-20 01:56:20.599321 INFO::Verifying options selected are valid
2026-02-20 01:56:22.987576 INFO::Writing function arguments to log file
2026-02-20 01:56:23.00048 INFO::Verifying options selected are valid
2026-02-20 01:56:23.001707 INFO::Determining format of input files
2026-02-20 01:56:23.002762 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-20 01:56:23.005196 INFO::Running selected normalization method: TSS
2026-02-20 01:56:23.006735 INFO::Creating output feature tables folder
2026-02-20 01:56:23.007729 INFO::Writing normalized data to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/features/data_norm.tsv
2026-02-20 01:56:23.009249 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-20 01:56:23.010178 INFO::Total samples in data: 16
2026-02-20 01:56:23.011081 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-20 01:56:23.011984 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-20 01:56:23.014057 INFO::Total filtered features: 0
2026-02-20 01:56:23.015073 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-20 01:56:23.016292 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-20 01:56:23.017274 INFO::Filtered feature names from variance filtering:
2026-02-20 01:56:23.018202 INFO::Writing filtered data to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/features/filtered_data.tsv
2026-02-20 01:56:23.019814 INFO::Running selected transform method: LOG
2026-02-20 01:56:23.02106 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/features/data_transformed.tsv
2026-02-20 01:56:23.022781 INFO::Applying z-score to standardize continuous metadata
2026-02-20 01:56:23.027606 INFO::Running the linear model component
2026-02-20 01:56:23.042868 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:23.047893 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:23.052501 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:23.060272 INFO::Counting total values for each feature
2026-02-20 01:56:23.062293 INFO::Running the logistic model component
2026-02-20 01:56:23.077206 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:23.084405 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:23.091124 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:23.100858 INFO::Counting total values for each feature
2026-02-20 01:56:23.103498 INFO::Re-running abundances for warn_prevalence
2026-02-20 01:56:23.104629 INFO::Running selected normalization method: TSS
2026-02-20 01:56:23.106263 INFO::Running selected transform method: LOG
2026-02-20 01:56:23.12128 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:23.126188 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:23.130732 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:23.213068 INFO::Creating fits folder
2026-02-20 01:56:23.214387 INFO::Writing residuals to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/fits/residuals_linear.rds
2026-02-20 01:56:23.215622 INFO::Writing fitted values to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/fits/fitted_linear.rds
2026-02-20 01:56:23.216882 INFO::Writing residuals to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/fits/residuals_logistic.rds
2026-02-20 01:56:23.21812 INFO::Writing fitted values to file /tmp/RtmpQeV9fY/file1b2c3130a9e607/fits/fitted_logistic.rds
2026-02-20 01:56:23.220645 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpQeV9fY/file1b2c3130a9e607/all_results.tsv
2026-02-20 01:56:23.222429 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/RtmpQeV9fY/file1b2c3130a9e607/significant_results.tsv
2026-02-20 01:56:23.223832 INFO::Creating output figures folder
2026-02-20 01:56:23.22525 INFO::Writing summary plot of significant
results to file: /tmp/RtmpQeV9fY/file1b2c3130a9e607/figures/summary_plot.pdf
2026-02-20 01:56:24.916879 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpQeV9fY/file1b2c3130a9e607/figures
2026-02-20 01:56:24.918949 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-20 01:56:24.924242 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-20 01:56:25.464074 INFO::Writing summary plot of
significant results to file: /tmp/RtmpQeV9fY/file1b2c3130a9e607/figures/summary_plot.pdf
2026-02-20 01:56:27.10971 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpQeV9fY/file1b2c3130a9e607/figures
2026-02-20 01:56:27.111438 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-20 01:56:27.116817 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-20 01:56:27.679542 INFO::Running the linear model component
2026-02-20 01:56:27.689118 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:27.693805 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:27.698348 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:27.706264 INFO::Counting total values for each feature
2026-02-20 01:56:27.708205 INFO::Running the logistic model component
2026-02-20 01:56:27.717589 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:27.724234 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:27.731274 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:27.741698 INFO::Counting total values for each feature
2026-02-20 01:56:27.744073 INFO::Re-running abundances for warn_prevalence
2026-02-20 01:56:27.745045 INFO::Running selected normalization method: TSS
2026-02-20 01:56:27.746588 INFO::Running selected transform method: LOG
2026-02-20 01:56:27.756254 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:27.761591 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:27.766347 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:27.847696 INFO::Creating output folder
2026-02-20 01:56:27.848724 INFO::Creating output figures folder
2026-02-20 01:56:27.850019 INFO::Writing summary plot of significant
results to file: /tmp/RtmpQeV9fY/file1b2c3149f540c5/figures/summary_plot.pdf
2026-02-20 01:56:29.464834 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpQeV9fY/file1b2c3149f540c5/figures
2026-02-20 01:56:29.466487 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-20 01:56:29.471293 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-20 01:56:30.432217 INFO::Applying z-score to standardize continuous metadata
2026-02-20 01:56:30.439705 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-20 01:56:30.44065 INFO::Bypass z-score application to metadata
2026-02-20 01:56:30.443469 INFO::Bypass z-score application to metadata
2026-02-20 01:56:30.46392 INFO::Determining format of input files
2026-02-20 01:56:30.46522 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-20 01:56:30.466249 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-20 01:56:30.475051 INFO::Determining format of input files
2026-02-20 01:56:30.476175 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-20 01:56:30.477577 INFO::Input format is feature_specific_covariate samples as columns
2026-02-20 01:56:30.500876 INFO::Determining format of input files
2026-02-20 01:56:30.502348 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-20 01:56:30.503874 INFO::Input format is feature_specific_covariate samples as columns
2026-02-20 01:56:30.505928 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-20 01:56:30.506731 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-20 01:56:30.519197 INFO::Running selected transform method: LOG
2026-02-20 01:56:30.520439 INFO::Creating output feature tables folder
2026-02-20 01:56:30.521341 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQeV9fY/file1b2c312602eb50/features/data_transformed.tsv
2026-02-20 01:56:30.525407 INFO::Running selected transform method: LOG
2026-02-20 01:56:30.526523 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQeV9fY/file1b2c312602eb50/features/data_transformed.tsv
2026-02-20 01:56:30.530686 INFO::Running selected transform method: PLOG
2026-02-20 01:56:30.532402 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQeV9fY/file1b2c312602eb50/features/data_transformed.tsv
2026-02-20 01:56:30.535578 INFO::Running selected transform method: NONE
2026-02-20 01:56:30.536339 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpQeV9fY/file1b2c312602eb50/features/data_transformed.tsv
2026-02-20 01:56:30.544093 INFO::Running the linear model component
2026-02-20 01:56:30.552607 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:30.556814 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:30.560819 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:30.567725 INFO::Counting total values for each feature
2026-02-20 01:56:30.569326 INFO::Running the logistic model component
2026-02-20 01:56:30.577894 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:30.584548 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:30.590714 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:30.599825 INFO::Counting total values for each feature
2026-02-20 01:56:30.601904 INFO::Re-running abundances for warn_prevalence
2026-02-20 01:56:30.602731 INFO::Running selected normalization method: TSS
2026-02-20 01:56:30.604124 INFO::Running selected transform method: LOG
2026-02-20 01:56:30.612746 INFO::Fitting model to feature number 1, a
2026-02-20 01:56:30.617033 INFO::Fitting model to feature number 2, b
2026-02-20 01:56:30.621046 INFO::Fitting model to feature number 3, c
2026-02-20 01:56:30.699271 INFO::Creating output folder
2026-02-20 01:56:30.700294 INFO::Creating fits folder
2026-02-20 01:56:30.701185 INFO::Writing residuals to file /tmp/RtmpQeV9fY/file1b2c31737b67b2/fits/residuals_linear.rds
2026-02-20 01:56:30.70217 INFO::Writing fitted values to file /tmp/RtmpQeV9fY/file1b2c31737b67b2/fits/fitted_linear.rds
2026-02-20 01:56:30.703257 INFO::Writing residuals to file /tmp/RtmpQeV9fY/file1b2c31737b67b2/fits/residuals_logistic.rds
2026-02-20 01:56:30.7043 INFO::Writing fitted values to file /tmp/RtmpQeV9fY/file1b2c31737b67b2/fits/fitted_logistic.rds
2026-02-20 01:56:30.706591 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpQeV9fY/file1b2c31737b67b2/all_results.tsv
2026-02-20 01:56:30.708074 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/RtmpQeV9fY/file1b2c31737b67b2/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
361.975 5.170 367.126
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.851 | 0.481 | 20.335 | |
| maaslin_check_arguments | 0.145 | 0.000 | 0.145 | |
| maaslin_check_formula | 0.172 | 0.004 | 0.175 | |
| maaslin_compute_formula | 0.162 | 0.000 | 0.163 | |
| maaslin_contrast_test | 19.089 | 0.469 | 19.561 | |
| maaslin_filter | 0.462 | 0.037 | 0.499 | |
| maaslin_fit | 13.409 | 0.112 | 13.524 | |
| maaslin_log_arguments | 0.128 | 0.002 | 0.131 | |
| maaslin_normalize | 0.256 | 0.004 | 0.260 | |
| maaslin_plot_results | 43.480 | 0.170 | 43.616 | |
| maaslin_plot_results_from_output | 43.613 | 0.284 | 43.902 | |
| maaslin_process_metadata | 0.455 | 0.008 | 0.462 | |
| maaslin_read_data | 0.128 | 0.003 | 0.130 | |
| maaslin_reorder_data | 0.141 | 0.001 | 0.141 | |
| maaslin_transform | 0.548 | 0.023 | 0.571 | |
| maaslin_write_results | 13.545 | 0.118 | 13.665 | |
| maaslin_write_results_lefse_format | 15.296 | 0.148 | 15.445 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |