William Nickols
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-21 11:38 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 1154/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-20 22:06:03 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 22:20:05 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 841.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 50.655 1.189 52.376
maaslin_plot_results 49.287 1.034 50.682
maaslin3 21.703 1.005 22.977
maaslin_contrast_test 21.524 1.130 22.834
maaslin_write_results_lefse_format 17.715 0.803 18.851
maaslin_write_results 16.255 0.620 17.113
maaslin_fit 14.788 0.777 15.682
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-20 22:13:14.978205 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:13:15.096777 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:13:15.225139 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:13:15.25669 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:13:15.30232 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:13:15.417234 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:13:15.424128 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:13:15.437141 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:13:15.559784 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:13:15.566766 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:13:15.638089 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:13:15.706055 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:13:15.721595 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:13:15.766411 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:13:15.852506 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:13:33.242731 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:13:33.333875 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:13:33.423892 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:13:33.453166 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:13:33.499498 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:13:33.617251 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:13:33.624327 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:13:33.642185 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:13:33.764377 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:13:33.770603 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:13:33.833752 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:13:33.879217 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:13:33.896637 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:13:33.95319 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:13:34.041556 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:13:38.884 R[71041:58579887] XType: Using static font registry.
2025-11-20 22:14:02.504628 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:14:02.608455 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:14:02.711453 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:14:02.740475 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:14:02.784109 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:14:02.885164 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:14:02.894194 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:14:02.91664 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:14:03.063122 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:14:03.072598 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:14:03.145431 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:14:03.206679 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:14:03.224898 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:14:03.285913 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:14:03.394264 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:14:18.563472 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:14:18.66664 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:14:18.78738 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:14:18.81197 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:14:18.856547 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:14:18.942708 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:14:18.948957 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:14:18.967322 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:14:19.099483 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:14:19.105323 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:14:19.166982 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:14:19.214896 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:14:19.22786 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:14:19.27697 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:14:19.351883 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:14:19.572898 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115817478ad15/fits/residuals_linear.rds
2025-11-20 22:14:19.635666 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115817478ad15/fits/fitted_linear.rds
2025-11-20 22:14:19.703531 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115817478ad15/fits/residuals_logistic.rds
2025-11-20 22:14:20.027405 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115817478ad15/fits/fitted_logistic.rds
2025-11-20 22:14:45.139221 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:14:45.23965 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:14:45.343501 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:14:45.37378 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:14:45.41746 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:14:45.513453 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:14:45.521653 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:14:45.534996 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:14:45.651392 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:14:45.658569 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:14:45.721683 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:14:45.776056 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:14:45.793209 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:14:45.848793 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:14:45.936374 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:15:00.902891 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:15:01.002144 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:15:01.097543 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:15:01.19655 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:15:01.237027 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:15:01.334356 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:15:01.341131 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:15:01.35399 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:15:01.461949 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:15:01.468671 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:15:01.525336 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:15:01.574404 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:15:01.591693 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:15:01.642548 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:15:01.722761 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:15:01.968772 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115817478ad15/fits/residuals_linear.rds
2025-11-20 22:15:02.032185 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115817478ad15/fits/fitted_linear.rds
2025-11-20 22:15:02.091874 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115817478ad15/fits/residuals_logistic.rds
2025-11-20 22:15:02.384403 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115817478ad15/fits/fitted_logistic.rds
2025-11-20 22:15:26.708917 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:15:26.802824 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:15:26.88949 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:15:26.918687 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:15:26.963902 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:15:27.063505 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:15:27.071009 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:15:27.08428 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:15:27.199123 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:15:27.20646 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:15:27.265331 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:15:27.321547 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:15:27.339968 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:15:27.389373 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:15:27.469658 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:15:39.754489 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:15:39.852888 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:15:39.956542 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:15:39.985776 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:15:40.033314 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:15:40.135717 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:15:40.143649 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:15:40.157439 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:15:40.284834 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:15:40.291944 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:15:40.350002 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:15:40.399047 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:15:40.414166 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:15:40.46293 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:15:40.548416 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:15:40.81255 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115817478ad15/fits/residuals_linear.rds
2025-11-20 22:15:40.875484 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115817478ad15/fits/fitted_linear.rds
2025-11-20 22:15:40.942303 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115817478ad15/fits/residuals_logistic.rds
2025-11-20 22:15:41.267543 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115817478ad15/fits/fitted_logistic.rds
2025-11-20 22:16:06.619635 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:16:06.72345 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:16:06.816278 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:16:06.83998 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:16:06.880642 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:16:06.962224 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:16:06.968157 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:16:06.981571 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:16:07.111313 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:16:07.119106 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:16:07.183115 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:16:07.230181 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:16:07.243682 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:16:07.295887 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:16:07.396044 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:16:20.351925 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:16:20.446916 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:16:20.539017 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:16:20.567322 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:16:20.664181 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:16:20.762918 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:16:20.771292 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:16:20.786184 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:16:20.912873 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:16:20.919289 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:16:20.979766 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:16:21.026575 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:16:21.041089 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:16:21.103063 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:16:21.199866 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:16:49.524086 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:16:59.316158 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:17:26.864903 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:17:37.755301 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:17:38.504524 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_linear.rds
2025-11-20 22:17:38.570871 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_linear.rds
2025-11-20 22:17:38.613469 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_logistic.rds
2025-11-20 22:17:38.683978 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_logistic.rds
2025-11-20 22:18:04.774316 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:18:11.197555 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:18:11.59722 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_linear.rds
2025-11-20 22:18:11.665299 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_linear.rds
2025-11-20 22:18:11.705773 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_logistic.rds
2025-11-20 22:18:11.780583 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_logistic.rds
2025-11-20 22:18:33.596813 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:18:40.8185 WARNING::Fitting problem for feature 124 returning NA
2025-11-20 22:18:41.217174 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_linear.rds
2025-11-20 22:18:41.280485 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_linear.rds
2025-11-20 22:18:41.322672 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_logistic.rds
2025-11-20 22:18:41.393739 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_logistic.rds
2025-11-20 22:19:01.73488 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:19:01.822851 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:19:01.90837 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:19:01.93456 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:19:03.055019 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:19:03.134592 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:19:03.140476 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:19:03.15365 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:19:03.251856 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:19:03.257552 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:19:03.315396 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:19:03.365716 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:19:03.379414 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:19:03.428065 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:19:03.502671 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:19:16.098484 WARNING::Fitting problem for feature 50 returning NA
2025-11-20 22:19:16.188298 WARNING::Fitting problem for feature 62 returning NA
2025-11-20 22:19:16.268818 WARNING::Fitting problem for feature 74 returning NA
2025-11-20 22:19:16.289535 WARNING::Fitting problem for feature 78 returning NA
2025-11-20 22:19:16.322725 WARNING::Fitting problem for feature 84 returning NA
2025-11-20 22:19:16.417148 WARNING::Fitting problem for feature 96 returning NA
2025-11-20 22:19:16.423549 WARNING::Fitting problem for feature 97 returning NA
2025-11-20 22:19:16.439273 WARNING::Fitting problem for feature 99 returning NA
2025-11-20 22:19:16.554637 WARNING::Fitting problem for feature 114 returning NA
2025-11-20 22:19:16.563087 WARNING::Fitting problem for feature 115 returning NA
2025-11-20 22:19:16.628542 WARNING::Fitting problem for feature 123 returning NA
2025-11-20 22:19:16.684872 WARNING::Fitting problem for feature 130 returning NA
2025-11-20 22:19:16.702648 WARNING::Fitting problem for feature 132 returning NA
2025-11-20 22:19:16.761831 WARNING::Fitting problem for feature 139 returning NA
2025-11-20 22:19:16.848612 WARNING::Fitting problem for feature 150 returning NA
2025-11-20 22:19:17.193977 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_linear.rds
2025-11-20 22:19:17.253466 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_linear.rds
2025-11-20 22:19:17.321298 WARNING::Deleting existing residuals file: /tmp/RtmpIenKD3/file115811ab76686/fits/residuals_logistic.rds
2025-11-20 22:19:17.649808 WARNING::Deleting existing fitted file: /tmp/RtmpIenKD3/file115811ab76686/fits/fitted_logistic.rds
2025-11-20 22:19:40.300926 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-20 22:19:40.317 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-20 22:19:40.331774 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-20 22:19:40.39479 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-20 22:19:40.414367 ERROR::Effect name not found in metadata: d
2025-11-20 22:19:40.428731 ERROR::No user formula provided
2025-11-20 22:19:40.468728 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-20 22:19:40.481421 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-20 22:19:43.606305 INFO::Writing function arguments to log file
2025-11-20 22:19:43.632258 INFO::Verifying options selected are valid
2025-11-20 22:19:46.266729 INFO::Writing function arguments to log file
2025-11-20 22:19:46.285873 INFO::Verifying options selected are valid
2025-11-20 22:19:46.287326 INFO::Determining format of input files
2025-11-20 22:19:46.288362 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-20 22:19:46.290831 INFO::Running selected normalization method: TSS
2025-11-20 22:19:46.292655 INFO::Creating output feature tables folder
2025-11-20 22:19:46.293857 INFO::Writing normalized data to file /tmp/RtmpIenKD3/file11581112a69fe/features/data_norm.tsv
2025-11-20 22:19:46.29571 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-20 22:19:46.296727 INFO::Total samples in data: 16
2025-11-20 22:19:46.297967 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-20 22:19:46.298874 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-20 22:19:46.300727 INFO::Total filtered features: 0
2025-11-20 22:19:46.301759 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-20 22:19:46.303101 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-20 22:19:46.304645 INFO::Filtered feature names from variance filtering:
2025-11-20 22:19:46.305657 INFO::Writing filtered data to file /tmp/RtmpIenKD3/file11581112a69fe/features/filtered_data.tsv
2025-11-20 22:19:46.307506 INFO::Running selected transform method: LOG
2025-11-20 22:19:46.308753 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIenKD3/file11581112a69fe/features/data_transformed.tsv
2025-11-20 22:19:46.310554 INFO::Applying z-score to standardize continuous metadata
2025-11-20 22:19:46.31586 INFO::Running the linear model component
2025-11-20 22:19:46.340062 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:46.345427 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:46.35164 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:46.359543 INFO::Counting total values for each feature
2025-11-20 22:19:46.362663 INFO::Running the logistic model component
2025-11-20 22:19:46.387388 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:46.395191 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:46.402433 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:46.413211 INFO::Counting total values for each feature
2025-11-20 22:19:46.415842 INFO::Re-running abundances for warn_prevalence
2025-11-20 22:19:46.417046 INFO::Running selected normalization method: TSS
2025-11-20 22:19:46.419077 INFO::Running selected transform method: LOG
2025-11-20 22:19:46.443413 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:46.447859 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:46.452091 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:46.551231 INFO::Creating fits folder
2025-11-20 22:19:46.553536 INFO::Writing residuals to file /tmp/RtmpIenKD3/file11581112a69fe/fits/residuals_linear.rds
2025-11-20 22:19:46.555757 INFO::Writing fitted values to file /tmp/RtmpIenKD3/file11581112a69fe/fits/fitted_linear.rds
2025-11-20 22:19:46.55764 INFO::Writing residuals to file /tmp/RtmpIenKD3/file11581112a69fe/fits/residuals_logistic.rds
2025-11-20 22:19:46.559247 INFO::Writing fitted values to file /tmp/RtmpIenKD3/file11581112a69fe/fits/fitted_logistic.rds
2025-11-20 22:19:46.563637 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpIenKD3/file11581112a69fe/all_results.tsv
2025-11-20 22:19:46.566267 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/RtmpIenKD3/file11581112a69fe/significant_results.tsv
2025-11-20 22:19:46.56845 INFO::Creating output figures folder
2025-11-20 22:19:46.570123 INFO::Writing summary plot of significant
results to file: /tmp/RtmpIenKD3/file11581112a69fe/figures/summary_plot.pdf
2025-11-20 22:19:48.320552 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpIenKD3/file11581112a69fe/figures
2025-11-20 22:19:48.323438 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-20 22:19:48.330058 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-20 22:19:48.912408 INFO::Writing summary plot of
significant results to file: /tmp/RtmpIenKD3/file11581112a69fe/figures/summary_plot.pdf
2025-11-20 22:19:50.692386 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpIenKD3/file11581112a69fe/figures
2025-11-20 22:19:50.694776 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-20 22:19:50.701252 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-20 22:19:51.325209 INFO::Running the linear model component
2025-11-20 22:19:51.336643 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:51.343535 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:51.34928 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:51.357929 INFO::Counting total values for each feature
2025-11-20 22:19:51.360157 INFO::Running the logistic model component
2025-11-20 22:19:51.371137 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:51.377772 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:51.383529 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:51.392534 INFO::Counting total values for each feature
2025-11-20 22:19:51.395629 INFO::Re-running abundances for warn_prevalence
2025-11-20 22:19:51.39644 INFO::Running selected normalization method: TSS
2025-11-20 22:19:51.397743 INFO::Running selected transform method: LOG
2025-11-20 22:19:51.408119 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:51.412715 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:51.416663 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:51.520956 INFO::Creating output folder
2025-11-20 22:19:51.522488 INFO::Creating output figures folder
2025-11-20 22:19:51.524381 INFO::Writing summary plot of significant
results to file: /tmp/RtmpIenKD3/file115811db4f19e/figures/summary_plot.pdf
2025-11-20 22:19:53.400074 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpIenKD3/file115811db4f19e/figures
2025-11-20 22:19:53.401922 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-20 22:19:53.407707 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-20 22:19:54.588776 INFO::Applying z-score to standardize continuous metadata
2025-11-20 22:19:54.597947 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-20 22:19:54.599218 INFO::Bypass z-score application to metadata
2025-11-20 22:19:54.603005 INFO::Bypass z-score application to metadata
2025-11-20 22:19:54.629154 INFO::Determining format of input files
2025-11-20 22:19:54.630442 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-20 22:19:54.631802 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-20 22:19:54.641708 INFO::Determining format of input files
2025-11-20 22:19:54.643305 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-20 22:19:54.644814 INFO::Input format is feature_specific_covariate samples as columns
2025-11-20 22:19:54.652991 INFO::Determining format of input files
2025-11-20 22:19:54.654182 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-20 22:19:54.655186 INFO::Input format is feature_specific_covariate samples as columns
2025-11-20 22:19:54.656683 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-20 22:19:54.657401 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-20 22:19:54.671355 INFO::Running selected transform method: LOG
2025-11-20 22:19:54.673036 INFO::Creating output feature tables folder
2025-11-20 22:19:54.674637 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIenKD3/file115814f1b4cf3/features/data_transformed.tsv
2025-11-20 22:19:54.680622 INFO::Running selected transform method: LOG
2025-11-20 22:19:54.681857 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIenKD3/file115814f1b4cf3/features/data_transformed.tsv
2025-11-20 22:19:54.687163 INFO::Running selected transform method: PLOG
2025-11-20 22:19:54.689361 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIenKD3/file115814f1b4cf3/features/data_transformed.tsv
2025-11-20 22:19:54.693765 INFO::Running selected transform method: NONE
2025-11-20 22:19:54.694992 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIenKD3/file115814f1b4cf3/features/data_transformed.tsv
2025-11-20 22:19:54.708722 INFO::Running the linear model component
2025-11-20 22:19:54.72241 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:54.728116 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:54.733064 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:54.743215 INFO::Counting total values for each feature
2025-11-20 22:19:54.74547 INFO::Running the logistic model component
2025-11-20 22:19:54.755683 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:54.76207 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:54.769504 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:54.779138 INFO::Counting total values for each feature
2025-11-20 22:19:54.781097 INFO::Re-running abundances for warn_prevalence
2025-11-20 22:19:54.78194 INFO::Running selected normalization method: TSS
2025-11-20 22:19:54.783229 INFO::Running selected transform method: LOG
2025-11-20 22:19:54.794605 INFO::Fitting model to feature number 1, a
2025-11-20 22:19:54.799351 INFO::Fitting model to feature number 2, b
2025-11-20 22:19:54.803851 INFO::Fitting model to feature number 3, c
2025-11-20 22:19:54.91857 INFO::Creating output folder
2025-11-20 22:19:54.920153 INFO::Creating fits folder
2025-11-20 22:19:54.921589 INFO::Writing residuals to file /tmp/RtmpIenKD3/file115819590e18/fits/residuals_linear.rds
2025-11-20 22:19:54.923246 INFO::Writing fitted values to file /tmp/RtmpIenKD3/file115819590e18/fits/fitted_linear.rds
2025-11-20 22:19:54.924804 INFO::Writing residuals to file /tmp/RtmpIenKD3/file115819590e18/fits/residuals_logistic.rds
2025-11-20 22:19:54.926343 INFO::Writing fitted values to file /tmp/RtmpIenKD3/file115819590e18/fits/fitted_logistic.rds
2025-11-20 22:19:54.929765 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpIenKD3/file115819590e18/all_results.tsv
2025-11-20 22:19:54.931487 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/RtmpIenKD3/file115819590e18/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
402.376 8.405 413.682
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 21.703 | 1.005 | 22.977 | |
| maaslin_check_arguments | 0.178 | 0.004 | 0.183 | |
| maaslin_check_formula | 0.166 | 0.010 | 0.177 | |
| maaslin_compute_formula | 0.179 | 0.012 | 0.192 | |
| maaslin_contrast_test | 21.524 | 1.130 | 22.834 | |
| maaslin_filter | 0.636 | 0.057 | 0.700 | |
| maaslin_fit | 14.788 | 0.777 | 15.682 | |
| maaslin_log_arguments | 0.169 | 0.010 | 0.182 | |
| maaslin_normalize | 0.353 | 0.023 | 0.380 | |
| maaslin_plot_results | 49.287 | 1.034 | 50.682 | |
| maaslin_plot_results_from_output | 50.655 | 1.189 | 52.376 | |
| maaslin_process_metadata | 0.686 | 0.047 | 0.738 | |
| maaslin_read_data | 0.181 | 0.011 | 0.194 | |
| maaslin_reorder_data | 0.175 | 0.011 | 0.188 | |
| maaslin_transform | 0.79 | 0.06 | 0.87 | |
| maaslin_write_results | 16.255 | 0.620 | 17.113 | |
| maaslin_write_results_lefse_format | 17.715 | 0.803 | 18.851 | |
| preprocess_dna_mtx | 0.004 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |