William Nickols
| Snapshot Date: 2026-02-25 13:45 -0500 (Wed, 25 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 2026-02-26 11:57 -0500 (Thu, 26 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: 2026-02-26 01:28:30 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 01:50:23 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 1313.4 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 43.982 0.294 44.239
maaslin_plot_results_from_output 43.810 0.391 44.207
maaslin3 20.309 0.495 20.806
maaslin_contrast_test 19.439 0.332 19.772
maaslin_write_results_lefse_format 14.035 0.050 14.084
maaslin_write_results 13.866 0.145 14.011
maaslin_fit 12.716 0.130 12.848
* 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")
2026-02-26 01:34:51.835794 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:34:51.920547 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:34:52.012451 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:34:52.033909 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:34:52.067666 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:34:52.142902 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:34:52.157313 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:34:52.169783 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:34:52.263359 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:34:52.277926 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:34:52.326989 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:34:52.381415 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:34:52.392922 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:34:52.431924 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:34:52.498758 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:35:08.223018 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:35:08.297832 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:35:08.373089 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:35:08.395261 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:35:08.430458 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:35:08.52392 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:35:08.529402 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:35:08.541695 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:35:08.640629 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:35:08.645966 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:35:08.694664 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:35:08.733711 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:35:08.745204 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:35:08.783836 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:35:08.851159 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:35:33.377565 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:35:33.451755 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:35:33.524875 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:35:33.546354 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:35:33.580287 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:35:33.655047 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:35:33.66049 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:35:33.672485 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:35:33.765436 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:35:33.770716 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:35:33.819996 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:35:33.86157 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:35:33.873912 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:35:33.915617 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:35:33.987267 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:35:46.94903 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:35:47.059823 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:35:47.138353 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:35:47.16044 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:35:47.195749 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:35:47.270788 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:35:47.276315 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:35:47.288273 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:35:47.387618 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:35:47.393025 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:35:47.443022 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:35:47.483721 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:35:47.49559 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:35:47.53704 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:35:47.608189 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:35:47.826563 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/residuals_linear.rds
2026-02-26 01:35:47.887352 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/fitted_linear.rds
2026-02-26 01:35:47.950083 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/residuals_logistic.rds
2026-02-26 01:35:48.249777 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/fitted_logistic.rds
2026-02-26 01:36:10.409312 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:36:10.486059 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:36:10.588747 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:36:10.610466 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:36:10.645198 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:36:10.720908 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:36:10.726343 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:36:10.738083 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:36:10.833328 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:36:10.838819 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:36:10.889916 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:36:10.931223 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:36:10.94303 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:36:10.982646 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:36:11.052669 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:36:23.102021 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:36:23.182303 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:36:23.26109 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:36:23.283936 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:36:23.31966 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:36:23.399345 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:36:23.404906 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:36:23.417076 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:36:23.515827 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:36:23.521441 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:36:23.57494 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:36:23.618317 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:36:23.631472 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:36:23.674688 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:36:23.748896 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:36:23.977414 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/residuals_linear.rds
2026-02-26 01:36:24.03905 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/fitted_linear.rds
2026-02-26 01:36:24.102206 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/residuals_logistic.rds
2026-02-26 01:36:24.401186 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/fitted_logistic.rds
2026-02-26 01:36:45.936004 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:36:46.019371 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:36:46.10059 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:36:46.125357 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:36:46.163273 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:36:46.267324 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:36:46.272961 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:36:46.285664 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:36:46.386681 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:36:46.392336 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:36:46.447022 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:36:46.490049 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:36:46.503127 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:36:46.546067 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:36:46.618643 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:36:58.737643 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:36:58.814727 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:36:58.891362 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:36:58.913548 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:36:58.94943 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:36:59.02669 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:36:59.032145 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:36:59.044392 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:36:59.143311 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:36:59.148883 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:36:59.202085 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:36:59.24538 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:36:59.257504 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:36:59.298606 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:36:59.369207 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:36:59.570236 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/residuals_linear.rds
2026-02-26 01:36:59.631308 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/fitted_linear.rds
2026-02-26 01:36:59.695123 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/residuals_logistic.rds
2026-02-26 01:36:59.995329 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc14e80885f/fits/fitted_logistic.rds
2026-02-26 01:37:21.542411 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:37:21.618946 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:37:21.696061 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:37:21.719934 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:37:21.760312 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:37:21.837992 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:37:21.843543 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:37:21.85623 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:37:21.958424 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:37:21.964272 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:37:22.018392 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:37:22.061641 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:37:22.074596 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:37:22.11806 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:37:22.1927 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:37:33.871001 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:37:33.946801 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:37:34.021164 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:37:34.04261 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:37:34.077295 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:37:34.152229 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:37:34.157535 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:37:34.169151 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:37:34.263294 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:37:34.268723 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:37:34.31849 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:37:34.359067 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:37:34.371281 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:37:34.410919 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:37:34.478638 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:37:58.379965 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:38:08.131934 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:38:32.920742 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:38:42.973426 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:38:43.589892 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_linear.rds
2026-02-26 01:38:43.651698 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_linear.rds
2026-02-26 01:38:43.690041 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_logistic.rds
2026-02-26 01:38:43.758835 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_logistic.rds
2026-02-26 01:39:07.577932 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:39:13.906966 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:39:14.226523 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_linear.rds
2026-02-26 01:39:14.289111 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_linear.rds
2026-02-26 01:39:14.328091 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_logistic.rds
2026-02-26 01:39:14.3984 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_logistic.rds
2026-02-26 01:39:33.168873 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:39:40.416692 WARNING::Fitting problem for feature 124 returning NA
2026-02-26 01:39:40.744412 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_linear.rds
2026-02-26 01:39:40.806059 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_linear.rds
2026-02-26 01:39:40.844906 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_logistic.rds
2026-02-26 01:39:40.914416 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_logistic.rds
2026-02-26 01:39:59.055996 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:39:59.138933 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:39:59.223313 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:39:59.248618 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:39:59.28693 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:39:59.39142 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:39:59.397161 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:39:59.409749 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:39:59.507643 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:39:59.51326 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:39:59.564207 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:39:59.605006 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:39:59.617019 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:39:59.65759 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:39:59.72755 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:40:12.527776 WARNING::Fitting problem for feature 50 returning NA
2026-02-26 01:40:12.603027 WARNING::Fitting problem for feature 62 returning NA
2026-02-26 01:40:12.676953 WARNING::Fitting problem for feature 74 returning NA
2026-02-26 01:40:12.698856 WARNING::Fitting problem for feature 78 returning NA
2026-02-26 01:40:12.73396 WARNING::Fitting problem for feature 84 returning NA
2026-02-26 01:40:12.80994 WARNING::Fitting problem for feature 96 returning NA
2026-02-26 01:40:12.81546 WARNING::Fitting problem for feature 97 returning NA
2026-02-26 01:40:12.827481 WARNING::Fitting problem for feature 99 returning NA
2026-02-26 01:40:12.925797 WARNING::Fitting problem for feature 114 returning NA
2026-02-26 01:40:12.931944 WARNING::Fitting problem for feature 115 returning NA
2026-02-26 01:40:12.985474 WARNING::Fitting problem for feature 123 returning NA
2026-02-26 01:40:13.02825 WARNING::Fitting problem for feature 130 returning NA
2026-02-26 01:40:13.040321 WARNING::Fitting problem for feature 132 returning NA
2026-02-26 01:40:13.080908 WARNING::Fitting problem for feature 139 returning NA
2026-02-26 01:40:13.150189 WARNING::Fitting problem for feature 150 returning NA
2026-02-26 01:40:13.422997 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_linear.rds
2026-02-26 01:40:13.483856 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_linear.rds
2026-02-26 01:40:13.546796 WARNING::Deleting existing residuals file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/residuals_logistic.rds
2026-02-26 01:40:13.845921 WARNING::Deleting existing fitted file: /tmp/Rtmp9z9jQu/file3c1bc15697f74/fits/fitted_logistic.rds
2026-02-26 01:40:35.169183 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-26 01:40:35.186845 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-26 01:40:35.198672 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-26 01:40:35.25237 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-26 01:40:35.26952 ERROR::Effect name not found in metadata: d
2026-02-26 01:40:35.280804 ERROR::No user formula provided
2026-02-26 01:40:35.312346 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-26 01:40:35.324366 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-26 01:40:38.114322 INFO::Writing function arguments to log file
2026-02-26 01:40:38.128826 INFO::Verifying options selected are valid
2026-02-26 01:40:40.407697 INFO::Writing function arguments to log file
2026-02-26 01:40:40.419999 INFO::Verifying options selected are valid
2026-02-26 01:40:40.421102 INFO::Determining format of input files
2026-02-26 01:40:40.422087 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-26 01:40:40.424412 INFO::Running selected normalization method: TSS
2026-02-26 01:40:40.425886 INFO::Creating output feature tables folder
2026-02-26 01:40:40.426848 INFO::Writing normalized data to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/features/data_norm.tsv
2026-02-26 01:40:40.428313 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-26 01:40:40.429221 INFO::Total samples in data: 16
2026-02-26 01:40:40.430094 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-26 01:40:40.430957 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-26 01:40:40.432861 INFO::Total filtered features: 0
2026-02-26 01:40:40.433815 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-26 01:40:40.434952 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-26 01:40:40.435882 INFO::Filtered feature names from variance filtering:
2026-02-26 01:40:40.436738 INFO::Writing filtered data to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/features/filtered_data.tsv
2026-02-26 01:40:40.438179 INFO::Running selected transform method: LOG
2026-02-26 01:40:40.439353 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/features/data_transformed.tsv
2026-02-26 01:40:40.440967 INFO::Applying z-score to standardize continuous metadata
2026-02-26 01:40:40.445387 INFO::Running the linear model component
2026-02-26 01:40:40.45917 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:40.463621 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:40.467802 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:40.474803 INFO::Counting total values for each feature
2026-02-26 01:40:40.476651 INFO::Running the logistic model component
2026-02-26 01:40:40.490571 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:40.496912 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:40.50287 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:40.5116 INFO::Counting total values for each feature
2026-02-26 01:40:40.513703 INFO::Re-running abundances for warn_prevalence
2026-02-26 01:40:40.514626 INFO::Running selected normalization method: TSS
2026-02-26 01:40:40.516078 INFO::Running selected transform method: LOG
2026-02-26 01:40:40.529815 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:40.534147 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:40.538236 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:40.612105 INFO::Creating fits folder
2026-02-26 01:40:40.613266 INFO::Writing residuals to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/fits/residuals_linear.rds
2026-02-26 01:40:40.614397 INFO::Writing fitted values to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/fits/fitted_linear.rds
2026-02-26 01:40:40.615535 INFO::Writing residuals to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/fits/residuals_logistic.rds
2026-02-26 01:40:40.616691 INFO::Writing fitted values to file /tmp/Rtmp9z9jQu/file3c1bc14267f405/fits/fitted_logistic.rds
2026-02-26 01:40:40.618951 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9z9jQu/file3c1bc14267f405/all_results.tsv
2026-02-26 01:40:40.620552 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/Rtmp9z9jQu/file3c1bc14267f405/significant_results.tsv
2026-02-26 01:40:40.621875 INFO::Creating output figures folder
2026-02-26 01:40:40.623209 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9z9jQu/file3c1bc14267f405/figures/summary_plot.pdf
2026-02-26 01:40:42.216548 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9z9jQu/file3c1bc14267f405/figures
2026-02-26 01:40:42.218631 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-26 01:40:42.22409 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-26 01:40:42.790453 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp9z9jQu/file3c1bc14267f405/figures/summary_plot.pdf
2026-02-26 01:40:44.377603 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9z9jQu/file3c1bc14267f405/figures
2026-02-26 01:40:44.379168 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-26 01:40:44.384099 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-26 01:40:44.899654 INFO::Running the linear model component
2026-02-26 01:40:44.908693 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:44.913158 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:44.917209 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:44.924609 INFO::Counting total values for each feature
2026-02-26 01:40:44.926356 INFO::Running the logistic model component
2026-02-26 01:40:44.934868 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:44.941326 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:44.947213 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:44.955891 INFO::Counting total values for each feature
2026-02-26 01:40:44.957888 INFO::Re-running abundances for warn_prevalence
2026-02-26 01:40:44.95867 INFO::Running selected normalization method: TSS
2026-02-26 01:40:44.960039 INFO::Running selected transform method: LOG
2026-02-26 01:40:44.968745 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:44.972916 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:44.976896 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:45.054867 INFO::Creating output folder
2026-02-26 01:40:45.055839 INFO::Creating output figures folder
2026-02-26 01:40:45.057058 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9z9jQu/file3c1bc17dce58d3/figures/summary_plot.pdf
2026-02-26 01:40:46.670643 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9z9jQu/file3c1bc17dce58d3/figures
2026-02-26 01:40:46.672329 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-26 01:40:46.677339 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-26 01:40:47.639296 INFO::Applying z-score to standardize continuous metadata
2026-02-26 01:40:47.646547 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-26 01:40:47.647437 INFO::Bypass z-score application to metadata
2026-02-26 01:40:47.650141 INFO::Bypass z-score application to metadata
2026-02-26 01:40:47.669056 INFO::Determining format of input files
2026-02-26 01:40:47.670044 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-26 01:40:47.670898 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-26 01:40:47.678405 INFO::Determining format of input files
2026-02-26 01:40:47.679446 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-26 01:40:47.680741 INFO::Input format is feature_specific_covariate samples as columns
2026-02-26 01:40:47.688893 INFO::Determining format of input files
2026-02-26 01:40:47.689811 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-26 01:40:47.690833 INFO::Input format is feature_specific_covariate samples as columns
2026-02-26 01:40:47.692478 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-26 01:40:47.693276 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-26 01:40:47.705286 INFO::Running selected transform method: LOG
2026-02-26 01:40:47.70658 INFO::Creating output feature tables folder
2026-02-26 01:40:47.707532 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9z9jQu/file3c1bc161fb38ac/features/data_transformed.tsv
2026-02-26 01:40:47.711709 INFO::Running selected transform method: LOG
2026-02-26 01:40:47.71277 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9z9jQu/file3c1bc161fb38ac/features/data_transformed.tsv
2026-02-26 01:40:47.7318 INFO::Running selected transform method: PLOG
2026-02-26 01:40:47.733581 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9z9jQu/file3c1bc161fb38ac/features/data_transformed.tsv
2026-02-26 01:40:47.737065 INFO::Running selected transform method: NONE
2026-02-26 01:40:47.737875 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9z9jQu/file3c1bc161fb38ac/features/data_transformed.tsv
2026-02-26 01:40:47.745718 INFO::Running the linear model component
2026-02-26 01:40:47.754318 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:47.758539 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:47.762565 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:47.770116 INFO::Counting total values for each feature
2026-02-26 01:40:47.771807 INFO::Running the logistic model component
2026-02-26 01:40:47.780323 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:47.786685 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:47.792754 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:47.801583 INFO::Counting total values for each feature
2026-02-26 01:40:47.803589 INFO::Re-running abundances for warn_prevalence
2026-02-26 01:40:47.804362 INFO::Running selected normalization method: TSS
2026-02-26 01:40:47.805709 INFO::Running selected transform method: LOG
2026-02-26 01:40:47.814125 INFO::Fitting model to feature number 1, a
2026-02-26 01:40:47.81808 INFO::Fitting model to feature number 2, b
2026-02-26 01:40:47.821897 INFO::Fitting model to feature number 3, c
2026-02-26 01:40:47.896332 INFO::Creating output folder
2026-02-26 01:40:47.897271 INFO::Creating fits folder
2026-02-26 01:40:47.898087 INFO::Writing residuals to file /tmp/Rtmp9z9jQu/file3c1bc113ff1004/fits/residuals_linear.rds
2026-02-26 01:40:47.899045 INFO::Writing fitted values to file /tmp/Rtmp9z9jQu/file3c1bc113ff1004/fits/fitted_linear.rds
2026-02-26 01:40:47.900013 INFO::Writing residuals to file /tmp/Rtmp9z9jQu/file3c1bc113ff1004/fits/residuals_logistic.rds
2026-02-26 01:40:47.900986 INFO::Writing fitted values to file /tmp/Rtmp9z9jQu/file3c1bc113ff1004/fits/fitted_logistic.rds
2026-02-26 01:40:47.903125 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9z9jQu/file3c1bc113ff1004/all_results.tsv
2026-02-26 01:40:47.904578 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/Rtmp9z9jQu/file3c1bc113ff1004/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.285 4.795 367.078
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.309 | 0.495 | 20.806 | |
| maaslin_check_arguments | 0.143 | 0.002 | 0.145 | |
| maaslin_check_formula | 0.166 | 0.004 | 0.169 | |
| maaslin_compute_formula | 0.148 | 0.003 | 0.150 | |
| maaslin_contrast_test | 19.439 | 0.332 | 19.772 | |
| maaslin_filter | 0.452 | 0.037 | 0.489 | |
| maaslin_fit | 12.716 | 0.130 | 12.848 | |
| maaslin_log_arguments | 0.159 | 0.002 | 0.161 | |
| maaslin_normalize | 0.271 | 0.003 | 0.274 | |
| maaslin_plot_results | 43.982 | 0.294 | 44.239 | |
| maaslin_plot_results_from_output | 43.810 | 0.391 | 44.207 | |
| maaslin_process_metadata | 0.441 | 0.005 | 0.446 | |
| maaslin_read_data | 0.120 | 0.002 | 0.122 | |
| maaslin_reorder_data | 0.128 | 0.003 | 0.131 | |
| maaslin_transform | 0.541 | 0.010 | 0.551 | |
| maaslin_write_results | 13.866 | 0.145 | 14.011 | |
| maaslin_write_results_lefse_format | 14.035 | 0.050 | 14.084 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.004 | |