William Nickols
| Snapshot Date: 2026-02-24 13:45 -0500 (Tue, 24 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 2026-02-25 11:57 -0500 (Wed, 25 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: 2026-02-25 01:06:21 -0500 (Wed, 25 Feb 2026) |
| EndedAt: 2026-02-25 01:28:13 -0500 (Wed, 25 Feb 2026) |
| EllapsedTime: 1311.4 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 43.871 0.202 44.035
maaslin_plot_results_from_output 43.291 0.379 43.682
maaslin3 20.598 0.543 21.141
maaslin_contrast_test 19.275 0.429 19.704
maaslin_write_results_lefse_format 14.711 0.242 14.953
maaslin_write_results 13.645 0.110 13.755
maaslin_fit 12.760 0.058 12.821
* 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")
2026-02-25 01:12:41.173576 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:12:41.263012 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:12:41.378211 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:12:41.399806 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:12:41.435103 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:12:41.511114 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:12:41.523269 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:12:41.535103 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:12:41.630054 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:12:41.635341 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:12:41.685198 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:12:41.735471 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:12:41.748432 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:12:41.788902 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:12:41.858431 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:12:58.087937 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:12:58.161332 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:12:58.233437 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:12:58.254362 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:12:58.288552 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:12:58.375017 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:12:58.380219 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:12:58.391783 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:12:58.485601 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:12:58.490954 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:12:58.53993 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:12:58.578602 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:12:58.590048 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:12:58.629281 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:12:58.695703 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:13:23.376716 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:13:23.45573 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:13:23.534279 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:13:23.557388 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:13:23.592876 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:13:23.670292 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:13:23.675828 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:13:23.688105 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:13:23.786295 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:13:23.791895 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:13:23.843738 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:13:23.884543 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:13:23.896726 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:13:23.937996 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:13:24.008338 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:13:36.974656 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:13:37.08016 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:13:37.158076 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:13:37.18055 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:13:37.216224 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:13:37.298277 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:13:37.304224 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:13:37.317528 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:13:37.418978 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:13:37.424461 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:13:37.477793 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:13:37.521082 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:13:37.534322 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:13:37.575433 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:13:37.64519 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:13:37.85279 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/residuals_linear.rds
2026-02-25 01:13:37.914026 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/fitted_linear.rds
2026-02-25 01:13:37.977045 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/residuals_logistic.rds
2026-02-25 01:13:38.276729 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/fitted_logistic.rds
2026-02-25 01:14:00.781029 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:14:00.877899 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:14:01.002523 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:14:01.027727 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:14:01.067155 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:14:01.14997 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:14:01.156002 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:14:01.168698 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:14:01.274297 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:14:01.280336 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:14:01.333177 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:14:01.376662 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:14:01.389847 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:14:01.433668 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:14:01.508427 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:14:13.57602 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:14:13.659945 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:14:13.739822 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:14:13.763481 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:14:13.800286 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:14:13.877595 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:14:13.883112 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:14:13.895115 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:14:13.994925 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:14:14.000598 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:14:14.052882 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:14:14.094958 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:14:14.108128 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:14:14.152088 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:14:14.227093 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:14:14.443079 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/residuals_linear.rds
2026-02-25 01:14:14.505145 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/fitted_linear.rds
2026-02-25 01:14:14.568897 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/residuals_logistic.rds
2026-02-25 01:14:14.869001 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/fitted_logistic.rds
2026-02-25 01:14:36.533337 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:14:36.616172 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:14:36.698381 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:14:36.723376 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:14:36.761838 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:14:36.865869 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:14:36.871379 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:14:36.88392 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:14:36.987101 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:14:36.992967 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:14:37.045853 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:14:37.087987 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:14:37.100617 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:14:37.145165 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:14:37.221418 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:14:50.099473 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:14:50.175013 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:14:50.248436 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:14:50.270297 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:14:50.304793 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:14:50.382493 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:14:50.388065 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:14:50.399749 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:14:50.494265 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:14:50.499738 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:14:50.550753 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:14:50.598546 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:14:50.612421 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:14:50.657545 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:14:50.734698 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:14:50.961695 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/residuals_linear.rds
2026-02-25 01:14:51.022538 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/fitted_linear.rds
2026-02-25 01:14:51.08573 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/residuals_logistic.rds
2026-02-25 01:14:51.385087 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file1157137025ad30/fits/fitted_logistic.rds
2026-02-25 01:15:12.844622 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:15:12.926719 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:15:13.006872 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:15:13.030235 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:15:13.068062 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:15:13.14791 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:15:13.153736 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:15:13.166629 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:15:13.267546 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:15:13.273381 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:15:13.326712 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:15:13.401952 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:15:13.414572 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:15:13.45815 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:15:13.530596 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:15:24.729495 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:15:24.809642 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:15:24.886451 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:15:24.909317 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:15:24.944824 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:15:25.02258 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:15:25.028383 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:15:25.040951 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:15:25.13936 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:15:25.144959 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:15:25.196117 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:15:25.238257 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:15:25.25069 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:15:25.38675 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:15:25.459759 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:15:51.903443 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:16:00.950245 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:16:26.123549 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:16:36.132623 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:16:36.726469 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_linear.rds
2026-02-25 01:16:36.788553 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_linear.rds
2026-02-25 01:16:36.82767 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_logistic.rds
2026-02-25 01:16:36.896576 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_logistic.rds
2026-02-25 01:16:59.584593 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:17:04.790439 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:17:05.104544 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_linear.rds
2026-02-25 01:17:05.166618 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_linear.rds
2026-02-25 01:17:05.205573 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_logistic.rds
2026-02-25 01:17:05.275623 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_logistic.rds
2026-02-25 01:17:24.136636 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:17:30.503235 WARNING::Fitting problem for feature 124 returning NA
2026-02-25 01:17:30.803384 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_linear.rds
2026-02-25 01:17:30.864972 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_linear.rds
2026-02-25 01:17:30.903533 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_logistic.rds
2026-02-25 01:17:30.972822 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_logistic.rds
2026-02-25 01:17:50.015466 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:17:50.089855 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:17:50.1634 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:17:50.185175 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:17:50.219539 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:17:50.295517 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:17:50.300854 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:17:50.312933 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:17:50.40873 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:17:50.43207 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:17:50.489827 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:17:50.530286 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:17:50.542214 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:17:50.582645 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:17:50.652452 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:18:01.470949 WARNING::Fitting problem for feature 50 returning NA
2026-02-25 01:18:01.553328 WARNING::Fitting problem for feature 62 returning NA
2026-02-25 01:18:01.628978 WARNING::Fitting problem for feature 74 returning NA
2026-02-25 01:18:01.65019 WARNING::Fitting problem for feature 78 returning NA
2026-02-25 01:18:01.683448 WARNING::Fitting problem for feature 84 returning NA
2026-02-25 01:18:01.756338 WARNING::Fitting problem for feature 96 returning NA
2026-02-25 01:18:01.761583 WARNING::Fitting problem for feature 97 returning NA
2026-02-25 01:18:01.773041 WARNING::Fitting problem for feature 99 returning NA
2026-02-25 01:18:01.866975 WARNING::Fitting problem for feature 114 returning NA
2026-02-25 01:18:01.872451 WARNING::Fitting problem for feature 115 returning NA
2026-02-25 01:18:01.922595 WARNING::Fitting problem for feature 123 returning NA
2026-02-25 01:18:01.96339 WARNING::Fitting problem for feature 130 returning NA
2026-02-25 01:18:01.975484 WARNING::Fitting problem for feature 132 returning NA
2026-02-25 01:18:02.01644 WARNING::Fitting problem for feature 139 returning NA
2026-02-25 01:18:02.086282 WARNING::Fitting problem for feature 150 returning NA
2026-02-25 01:18:02.362359 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_linear.rds
2026-02-25 01:18:02.423571 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_linear.rds
2026-02-25 01:18:02.486527 WARNING::Deleting existing residuals file: /tmp/RtmpZDKz5M/file115713121dea40/fits/residuals_logistic.rds
2026-02-25 01:18:02.785512 WARNING::Deleting existing fitted file: /tmp/RtmpZDKz5M/file115713121dea40/fits/fitted_logistic.rds
2026-02-25 01:18:23.686445 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-25 01:18:23.703407 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-25 01:18:23.715107 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-25 01:18:23.768344 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-25 01:18:23.785621 ERROR::Effect name not found in metadata: d
2026-02-25 01:18:23.797939 ERROR::No user formula provided
2026-02-25 01:18:23.830004 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-25 01:18:23.841496 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-25 01:18:26.772142 INFO::Writing function arguments to log file
2026-02-25 01:18:26.786861 INFO::Verifying options selected are valid
2026-02-25 01:18:29.11296 INFO::Writing function arguments to log file
2026-02-25 01:18:29.125316 INFO::Verifying options selected are valid
2026-02-25 01:18:29.126389 INFO::Determining format of input files
2026-02-25 01:18:29.127382 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-25 01:18:29.129715 INFO::Running selected normalization method: TSS
2026-02-25 01:18:29.131155 INFO::Creating output feature tables folder
2026-02-25 01:18:29.132109 INFO::Writing normalized data to file /tmp/RtmpZDKz5M/file11571344cba21a/features/data_norm.tsv
2026-02-25 01:18:29.133562 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-25 01:18:29.134448 INFO::Total samples in data: 16
2026-02-25 01:18:29.135303 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-25 01:18:29.136166 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-25 01:18:29.138144 INFO::Total filtered features: 0
2026-02-25 01:18:29.139097 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-25 01:18:29.140242 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-25 01:18:29.141192 INFO::Filtered feature names from variance filtering:
2026-02-25 01:18:29.142083 INFO::Writing filtered data to file /tmp/RtmpZDKz5M/file11571344cba21a/features/filtered_data.tsv
2026-02-25 01:18:29.14358 INFO::Running selected transform method: LOG
2026-02-25 01:18:29.144762 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZDKz5M/file11571344cba21a/features/data_transformed.tsv
2026-02-25 01:18:29.146396 INFO::Applying z-score to standardize continuous metadata
2026-02-25 01:18:29.150954 INFO::Running the linear model component
2026-02-25 01:18:29.165087 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:29.169693 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:29.173996 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:29.181155 INFO::Counting total values for each feature
2026-02-25 01:18:29.182977 INFO::Running the logistic model component
2026-02-25 01:18:29.196866 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:29.203451 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:29.209854 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:29.219153 INFO::Counting total values for each feature
2026-02-25 01:18:29.221378 INFO::Re-running abundances for warn_prevalence
2026-02-25 01:18:29.222342 INFO::Running selected normalization method: TSS
2026-02-25 01:18:29.223871 INFO::Running selected transform method: LOG
2026-02-25 01:18:29.238177 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:29.242725 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:29.247007 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:29.326427 INFO::Creating fits folder
2026-02-25 01:18:29.327666 INFO::Writing residuals to file /tmp/RtmpZDKz5M/file11571344cba21a/fits/residuals_linear.rds
2026-02-25 01:18:29.328852 INFO::Writing fitted values to file /tmp/RtmpZDKz5M/file11571344cba21a/fits/fitted_linear.rds
2026-02-25 01:18:29.330086 INFO::Writing residuals to file /tmp/RtmpZDKz5M/file11571344cba21a/fits/residuals_logistic.rds
2026-02-25 01:18:29.331295 INFO::Writing fitted values to file /tmp/RtmpZDKz5M/file11571344cba21a/fits/fitted_logistic.rds
2026-02-25 01:18:29.333727 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpZDKz5M/file11571344cba21a/all_results.tsv
2026-02-25 01:18:29.335402 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/RtmpZDKz5M/file11571344cba21a/significant_results.tsv
2026-02-25 01:18:29.336782 INFO::Creating output figures folder
2026-02-25 01:18:29.338165 INFO::Writing summary plot of significant
results to file: /tmp/RtmpZDKz5M/file11571344cba21a/figures/summary_plot.pdf
2026-02-25 01:18:30.995889 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpZDKz5M/file11571344cba21a/figures
2026-02-25 01:18:30.997838 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-25 01:18:31.002899 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-25 01:18:31.520426 INFO::Writing summary plot of
significant results to file: /tmp/RtmpZDKz5M/file11571344cba21a/figures/summary_plot.pdf
2026-02-25 01:18:33.19914 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpZDKz5M/file11571344cba21a/figures
2026-02-25 01:18:33.200781 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-25 01:18:33.206015 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-25 01:18:33.74263 INFO::Running the linear model component
2026-02-25 01:18:33.751719 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:33.75626 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:33.760323 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:33.767295 INFO::Counting total values for each feature
2026-02-25 01:18:33.768976 INFO::Running the logistic model component
2026-02-25 01:18:33.77737 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:33.783641 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:33.789547 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:33.798528 INFO::Counting total values for each feature
2026-02-25 01:18:33.800653 INFO::Re-running abundances for warn_prevalence
2026-02-25 01:18:33.80146 INFO::Running selected normalization method: TSS
2026-02-25 01:18:33.80288 INFO::Running selected transform method: LOG
2026-02-25 01:18:33.811528 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:33.815766 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:33.819775 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:33.899298 INFO::Creating output folder
2026-02-25 01:18:33.900332 INFO::Creating output figures folder
2026-02-25 01:18:33.901608 INFO::Writing summary plot of significant
results to file: /tmp/RtmpZDKz5M/file11571311a9d1fb/figures/summary_plot.pdf
2026-02-25 01:18:35.59287 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpZDKz5M/file11571311a9d1fb/figures
2026-02-25 01:18:35.594789 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-25 01:18:35.600207 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-25 01:18:36.587085 INFO::Applying z-score to standardize continuous metadata
2026-02-25 01:18:36.594705 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-25 01:18:36.595658 INFO::Bypass z-score application to metadata
2026-02-25 01:18:36.598362 INFO::Bypass z-score application to metadata
2026-02-25 01:18:36.618455 INFO::Determining format of input files
2026-02-25 01:18:36.619564 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-25 01:18:36.620471 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-25 01:18:36.628413 INFO::Determining format of input files
2026-02-25 01:18:36.629447 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-25 01:18:36.630754 INFO::Input format is feature_specific_covariate samples as columns
2026-02-25 01:18:36.652431 INFO::Determining format of input files
2026-02-25 01:18:36.653754 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-25 01:18:36.655146 INFO::Input format is feature_specific_covariate samples as columns
2026-02-25 01:18:36.657356 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-25 01:18:36.658154 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-25 01:18:36.670077 INFO::Running selected transform method: LOG
2026-02-25 01:18:36.671223 INFO::Creating output feature tables folder
2026-02-25 01:18:36.672087 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZDKz5M/file1157136aa8c47b/features/data_transformed.tsv
2026-02-25 01:18:36.67601 INFO::Running selected transform method: LOG
2026-02-25 01:18:36.677032 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZDKz5M/file1157136aa8c47b/features/data_transformed.tsv
2026-02-25 01:18:36.681046 INFO::Running selected transform method: PLOG
2026-02-25 01:18:36.682688 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZDKz5M/file1157136aa8c47b/features/data_transformed.tsv
2026-02-25 01:18:36.685644 INFO::Running selected transform method: NONE
2026-02-25 01:18:36.686383 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpZDKz5M/file1157136aa8c47b/features/data_transformed.tsv
2026-02-25 01:18:36.694186 INFO::Running the linear model component
2026-02-25 01:18:36.703229 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:36.70764 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:36.711606 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:36.718585 INFO::Counting total values for each feature
2026-02-25 01:18:36.720195 INFO::Running the logistic model component
2026-02-25 01:18:36.72857 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:36.734678 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:36.740456 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:36.74913 INFO::Counting total values for each feature
2026-02-25 01:18:36.751152 INFO::Re-running abundances for warn_prevalence
2026-02-25 01:18:36.751939 INFO::Running selected normalization method: TSS
2026-02-25 01:18:36.753296 INFO::Running selected transform method: LOG
2026-02-25 01:18:36.761822 INFO::Fitting model to feature number 1, a
2026-02-25 01:18:36.76599 INFO::Fitting model to feature number 2, b
2026-02-25 01:18:36.769977 INFO::Fitting model to feature number 3, c
2026-02-25 01:18:36.848183 INFO::Creating output folder
2026-02-25 01:18:36.849159 INFO::Creating fits folder
2026-02-25 01:18:36.850016 INFO::Writing residuals to file /tmp/RtmpZDKz5M/file115713529a4c98/fits/residuals_linear.rds
2026-02-25 01:18:36.850992 INFO::Writing fitted values to file /tmp/RtmpZDKz5M/file115713529a4c98/fits/fitted_linear.rds
2026-02-25 01:18:36.85207 INFO::Writing residuals to file /tmp/RtmpZDKz5M/file115713529a4c98/fits/residuals_logistic.rds
2026-02-25 01:18:36.853128 INFO::Writing fitted values to file /tmp/RtmpZDKz5M/file115713529a4c98/fits/fitted_logistic.rds
2026-02-25 01:18:36.855403 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpZDKz5M/file115713529a4c98/all_results.tsv
2026-02-25 01:18:36.856905 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/RtmpZDKz5M/file115713529a4c98/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
361.665 5.361 367.028
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.598 | 0.543 | 21.141 | |
| maaslin_check_arguments | 0.140 | 0.001 | 0.141 | |
| maaslin_check_formula | 0.160 | 0.002 | 0.163 | |
| maaslin_compute_formula | 0.144 | 0.001 | 0.145 | |
| maaslin_contrast_test | 19.275 | 0.429 | 19.704 | |
| maaslin_filter | 0.439 | 0.005 | 0.444 | |
| maaslin_fit | 12.760 | 0.058 | 12.821 | |
| maaslin_log_arguments | 0.134 | 0.000 | 0.134 | |
| maaslin_normalize | 0.263 | 0.003 | 0.266 | |
| maaslin_plot_results | 43.871 | 0.202 | 44.035 | |
| maaslin_plot_results_from_output | 43.291 | 0.379 | 43.682 | |
| maaslin_process_metadata | 0.473 | 0.023 | 0.496 | |
| maaslin_read_data | 0.137 | 0.001 | 0.138 | |
| maaslin_reorder_data | 0.133 | 0.003 | 0.136 | |
| maaslin_transform | 0.563 | 0.020 | 0.583 | |
| maaslin_write_results | 13.645 | 0.110 | 13.755 | |
| maaslin_write_results_lefse_format | 14.711 | 0.242 | 14.953 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.003 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |