William Nickols
| Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-04 12:05 -0400 (Thu, 04 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1149/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2025-09-03 21:47:15 -0400 (Wed, 03 Sep 2025) |
| EndedAt: 2025-09-03 22:00:05 -0400 (Wed, 03 Sep 2025) |
| EllapsedTime: 770.1 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* 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 41.943 1.057 43.290
maaslin_plot_results_from_output 41.597 0.913 42.773
maaslin3 23.767 1.054 25.064
maaslin_contrast_test 19.694 0.938 20.841
maaslin_write_results 16.690 0.864 17.681
maaslin_write_results_lefse_format 16.363 0.546 16.991
maaslin_fit 14.104 0.727 14.923
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.0’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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")
2025-09-03 21:54:07.511026 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:54:07.613693 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:54:07.72029 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:54:07.746982 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:54:07.796438 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:54:07.892922 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:54:07.899159 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:54:07.915458 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:54:08.052555 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:54:08.058773 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:54:08.111791 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:54:08.165687 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:54:08.182948 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:54:08.22687 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:54:08.314766 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:54:25.80851 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:54:25.925299 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:54:26.022407 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:54:26.051881 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:54:26.093766 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:54:26.179188 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:54:26.185797 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:54:26.202091 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:54:26.307405 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:54:26.31282 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:54:26.373023 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:54:26.422318 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:54:26.437903 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:54:26.492178 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:54:26.586421 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:54:30.416 R[4033:196230885] XType: com.apple.fonts is not accessible.
2025-09-03 21:54:30.417 R[4033:196230885] XType: XTFontStaticRegistry is enabled.
2025-09-03 21:54:47.526251 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:54:47.627161 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:54:47.771126 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:54:47.802347 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:54:47.851391 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:54:47.953817 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:54:47.961712 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:54:47.97789 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:54:48.098991 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:54:48.10442 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:54:48.162889 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:54:48.215125 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:54:48.229903 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:54:48.272509 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:54:48.400986 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:55:04.215177 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:55:04.329481 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:55:04.427919 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:55:04.45399 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:55:04.498008 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:55:04.605526 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:55:04.613871 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:55:04.629839 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:55:04.748601 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:55:04.757339 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:55:04.830362 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:55:04.890298 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:55:04.9071 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:55:04.963487 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:55:05.07053 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:55:05.380431 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/residuals_linear.rds
2025-09-03 21:55:05.447963 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/fitted_linear.rds
2025-09-03 21:55:05.522019 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/residuals_logistic.rds
2025-09-03 21:55:05.866932 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/fitted_logistic.rds
2025-09-03 21:55:25.105947 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:55:25.20946 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:55:25.303188 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:55:25.331808 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:55:25.375304 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:55:25.475448 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:55:25.48327 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:55:25.49823 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:55:25.634141 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:55:25.640949 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:55:25.708893 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:55:25.77647 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:55:25.795006 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:55:25.85328 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:55:25.961351 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:55:41.168259 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:55:41.267791 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:55:41.364633 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:55:41.393741 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:55:41.439518 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:55:41.552548 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:55:41.561652 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:55:41.580285 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:55:41.775713 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:55:41.783598 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:55:41.846504 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:55:41.896146 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:55:41.914316 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:55:41.972592 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:55:42.054809 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:55:42.290154 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/residuals_linear.rds
2025-09-03 21:55:42.364836 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/fitted_linear.rds
2025-09-03 21:55:42.43687 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/residuals_logistic.rds
2025-09-03 21:55:42.795443 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/fitted_logistic.rds
2025-09-03 21:56:01.57653 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:56:01.681154 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:56:01.789264 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:56:01.81995 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:56:01.862725 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:56:01.954049 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:56:01.962242 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:56:01.977122 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:56:02.099143 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:56:02.106367 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:56:02.165559 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:56:02.216623 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:56:02.230638 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:56:02.283028 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:56:02.362503 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:56:16.347261 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:56:16.450959 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:56:16.546202 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:56:16.573344 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:56:16.617892 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:56:16.705979 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:56:16.712893 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:56:16.725151 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:56:16.906352 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:56:16.913732 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:56:16.972908 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:56:17.02093 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:56:17.03475 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:56:17.085333 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:56:17.171573 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:56:17.415364 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/residuals_linear.rds
2025-09-03 21:56:17.48867 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/fitted_linear.rds
2025-09-03 21:56:17.562433 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/residuals_logistic.rds
2025-09-03 21:56:17.902355 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc177b0a0bb/fits/fitted_logistic.rds
2025-09-03 21:56:36.391413 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:56:36.493291 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:56:36.585335 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:56:36.612469 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:56:36.656976 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:56:36.752412 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:56:36.759192 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:56:36.773339 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:56:36.881197 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:56:36.887874 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:56:36.940133 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:56:36.990708 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:56:37.006333 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:56:37.061811 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:56:37.149568 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:56:51.108023 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:56:51.19218 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:56:51.279962 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:56:51.305533 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:56:51.346277 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:56:51.432075 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:56:51.438487 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:56:51.453841 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:56:51.557391 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:56:51.56586 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:56:51.630974 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:56:51.675158 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:56:51.68889 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:56:51.734725 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:56:51.823172 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:57:13.518699 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:57:24.532194 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:57:46.894909 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:57:58.427276 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:57:59.177233 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_linear.rds
2025-09-03 21:57:59.255952 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_linear.rds
2025-09-03 21:57:59.306066 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_logistic.rds
2025-09-03 21:57:59.387431 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_logistic.rds
2025-09-03 21:58:19.514088 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:58:26.537177 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:58:26.940085 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_linear.rds
2025-09-03 21:58:27.013221 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_linear.rds
2025-09-03 21:58:27.059753 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_logistic.rds
2025-09-03 21:58:27.129444 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_logistic.rds
2025-09-03 21:58:43.237022 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:58:50.589081 WARNING::Fitting problem for feature 124 returning NA
2025-09-03 21:58:50.972645 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_linear.rds
2025-09-03 21:58:51.040331 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_linear.rds
2025-09-03 21:58:51.085701 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_logistic.rds
2025-09-03 21:58:51.160145 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_logistic.rds
2025-09-03 21:59:07.189607 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:59:07.280359 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:59:07.403039 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:59:07.425596 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:59:07.460231 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:59:07.551345 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:59:07.556809 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:59:07.567707 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:59:07.679141 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:59:07.687414 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:59:07.746948 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:59:07.798184 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:59:07.814412 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:59:07.865678 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:59:07.946045 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:59:21.759215 WARNING::Fitting problem for feature 50 returning NA
2025-09-03 21:59:21.843336 WARNING::Fitting problem for feature 62 returning NA
2025-09-03 21:59:21.932027 WARNING::Fitting problem for feature 74 returning NA
2025-09-03 21:59:21.952353 WARNING::Fitting problem for feature 78 returning NA
2025-09-03 21:59:21.996855 WARNING::Fitting problem for feature 84 returning NA
2025-09-03 21:59:22.089626 WARNING::Fitting problem for feature 96 returning NA
2025-09-03 21:59:22.098098 WARNING::Fitting problem for feature 97 returning NA
2025-09-03 21:59:22.112158 WARNING::Fitting problem for feature 99 returning NA
2025-09-03 21:59:22.228182 WARNING::Fitting problem for feature 114 returning NA
2025-09-03 21:59:22.233485 WARNING::Fitting problem for feature 115 returning NA
2025-09-03 21:59:22.288777 WARNING::Fitting problem for feature 123 returning NA
2025-09-03 21:59:22.329937 WARNING::Fitting problem for feature 130 returning NA
2025-09-03 21:59:22.344542 WARNING::Fitting problem for feature 132 returning NA
2025-09-03 21:59:22.393497 WARNING::Fitting problem for feature 139 returning NA
2025-09-03 21:59:22.490439 WARNING::Fitting problem for feature 150 returning NA
2025-09-03 21:59:22.872862 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_linear.rds
2025-09-03 21:59:22.936814 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_linear.rds
2025-09-03 21:59:23.018961 WARNING::Deleting existing residuals file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/residuals_logistic.rds
2025-09-03 21:59:23.36492 WARNING::Deleting existing fitted file: /tmp/RtmpIBPeq6/filefc1177d1c9/fits/fitted_logistic.rds
2025-09-03 21:59:40.741333 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-03 21:59:40.758859 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-03 21:59:40.773549 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-03 21:59:40.837426 ERROR::No fixed, group, or
ordered effects included in formula.
2025-09-03 21:59:40.853728 ERROR::Effect name not found in metadata: d
2025-09-03 21:59:40.868273 ERROR::No user formula provided
2025-09-03 21:59:40.904272 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-03 21:59:40.919749 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-09-03 21:59:44.093251 INFO::Writing function arguments to log file
2025-09-03 21:59:44.118514 INFO::Verifying options selected are valid
2025-09-03 21:59:46.099007 INFO::Writing function arguments to log file
2025-09-03 21:59:46.119181 INFO::Verifying options selected are valid
2025-09-03 21:59:46.120377 INFO::Determining format of input files
2025-09-03 21:59:46.121614 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-03 21:59:46.12487 INFO::Running selected normalization method: TSS
2025-09-03 21:59:46.126471 INFO::Creating output feature tables folder
2025-09-03 21:59:46.127683 INFO::Writing normalized data to file /tmp/RtmpIBPeq6/filefc1aaa1991/features/data_norm.tsv
2025-09-03 21:59:46.12977 INFO::Filter data based on min abundance and min prevalence
2025-09-03 21:59:46.130909 INFO::Total samples in data: 16
2025-09-03 21:59:46.132033 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-03 21:59:46.134527 INFO::Total filtered features: 0
2025-09-03 21:59:46.135839 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-03 21:59:46.137087 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-03 21:59:46.138236 INFO::Filtered feature names from variance filtering:
2025-09-03 21:59:46.139284 INFO::Writing filtered data to file /tmp/RtmpIBPeq6/filefc1aaa1991/features/filtered_data.tsv
2025-09-03 21:59:46.141527 INFO::Running selected transform method: LOG
2025-09-03 21:59:46.143287 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIBPeq6/filefc1aaa1991/features/data_transformed.tsv
2025-09-03 21:59:46.145427 INFO::Applying z-score to standardize continuous metadata
2025-09-03 21:59:46.151592 INFO::Running the linear model component
2025-09-03 21:59:46.169888 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:46.175805 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:46.180747 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:46.189228 INFO::Counting total values for each feature
2025-09-03 21:59:46.191799 INFO::Running the logistic model component
2025-09-03 21:59:46.214389 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:46.220827 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:46.228144 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:46.237978 INFO::Counting total values for each feature
2025-09-03 21:59:46.240346 INFO::Re-running abundances for warn_prevalence
2025-09-03 21:59:46.241474 INFO::Running selected normalization method: TSS
2025-09-03 21:59:46.24332 INFO::Running selected transform method: LOG
2025-09-03 21:59:46.262741 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:46.269151 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:46.27514 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:46.378684 INFO::Creating fits folder
2025-09-03 21:59:46.380201 INFO::Writing residuals to file /tmp/RtmpIBPeq6/filefc1aaa1991/fits/residuals_linear.rds
2025-09-03 21:59:46.382478 INFO::Writing fitted values to file /tmp/RtmpIBPeq6/filefc1aaa1991/fits/fitted_linear.rds
2025-09-03 21:59:46.383919 INFO::Writing residuals to file /tmp/RtmpIBPeq6/filefc1aaa1991/fits/residuals_logistic.rds
2025-09-03 21:59:46.386173 INFO::Writing fitted values to file /tmp/RtmpIBPeq6/filefc1aaa1991/fits/fitted_logistic.rds
2025-09-03 21:59:46.390452 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpIBPeq6/filefc1aaa1991/all_results.tsv
2025-09-03 21:59:46.410849 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/RtmpIBPeq6/filefc1aaa1991/significant_results.tsv
2025-09-03 21:59:46.413268 INFO::Creating output figures folder
2025-09-03 21:59:46.415164 INFO::Writing summary plot of significant
results to file: /tmp/RtmpIBPeq6/filefc1aaa1991/figures/summary_plot.pdf
2025-09-03 21:59:47.72263 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpIBPeq6/filefc1aaa1991/figures
2025-09-03 21:59:47.725256 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-03 21:59:47.733757 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-03 21:59:48.192967 INFO::Writing summary plot of
significant results to file: /tmp/RtmpIBPeq6/filefc1aaa1991/figures/summary_plot.pdf
2025-09-03 21:59:49.640512 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpIBPeq6/filefc1aaa1991/figures
2025-09-03 21:59:49.642391 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-03 21:59:49.64892 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-03 21:59:50.1459 INFO::Running the linear model component
2025-09-03 21:59:50.157616 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:50.161661 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:50.166317 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:50.17485 INFO::Counting total values for each feature
2025-09-03 21:59:50.176658 INFO::Running the logistic model component
2025-09-03 21:59:50.189815 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:50.197615 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:50.205498 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:50.217042 INFO::Counting total values for each feature
2025-09-03 21:59:50.220104 INFO::Re-running abundances for warn_prevalence
2025-09-03 21:59:50.220926 INFO::Running selected normalization method: TSS
2025-09-03 21:59:50.222523 INFO::Running selected transform method: LOG
2025-09-03 21:59:50.231619 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:50.237964 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:50.243154 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:50.340987 INFO::Creating output folder
2025-09-03 21:59:50.342064 INFO::Creating output figures folder
2025-09-03 21:59:50.343336 INFO::Writing summary plot of significant
results to file: /tmp/RtmpIBPeq6/filefc1212f8ad/figures/summary_plot.pdf
2025-09-03 21:59:51.826959 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpIBPeq6/filefc1212f8ad/figures
2025-09-03 21:59:51.828947 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-03 21:59:51.835837 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-03 21:59:52.882551 INFO::Applying z-score to standardize continuous metadata
2025-09-03 21:59:52.891625 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-03 21:59:52.892476 INFO::Bypass z-score application to metadata
2025-09-03 21:59:52.895379 INFO::Bypass z-score application to metadata
2025-09-03 21:59:52.921134 INFO::Determining format of input files
2025-09-03 21:59:52.922024 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-03 21:59:52.922778 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-03 21:59:52.931134 INFO::Determining format of input files
2025-09-03 21:59:52.932172 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-03 21:59:52.933342 INFO::Input format is feature_specific_covariate samples as columns
2025-09-03 21:59:52.941246 INFO::Determining format of input files
2025-09-03 21:59:52.942623 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-03 21:59:52.944093 INFO::Input format is feature_specific_covariate samples as columns
2025-09-03 21:59:52.946301 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-03 21:59:52.947373 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-03 21:59:52.96388 INFO::Running selected transform method: LOG
2025-09-03 21:59:52.965586 INFO::Creating output feature tables folder
2025-09-03 21:59:52.967166 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIBPeq6/filefc126653b13/features/data_transformed.tsv
2025-09-03 21:59:52.971347 INFO::Running selected transform method: LOG
2025-09-03 21:59:52.972445 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIBPeq6/filefc126653b13/features/data_transformed.tsv
2025-09-03 21:59:52.976214 INFO::Running selected transform method: PLOG
2025-09-03 21:59:52.977647 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIBPeq6/filefc126653b13/features/data_transformed.tsv
2025-09-03 21:59:52.981813 INFO::Running selected transform method: NONE
2025-09-03 21:59:52.983018 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpIBPeq6/filefc126653b13/features/data_transformed.tsv
2025-09-03 21:59:52.994522 INFO::Running the linear model component
2025-09-03 21:59:53.006646 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:53.013685 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:53.018278 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:53.028326 INFO::Counting total values for each feature
2025-09-03 21:59:53.029993 INFO::Running the logistic model component
2025-09-03 21:59:53.043205 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:53.050578 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:53.056931 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:53.066455 INFO::Counting total values for each feature
2025-09-03 21:59:53.068439 INFO::Re-running abundances for warn_prevalence
2025-09-03 21:59:53.06927 INFO::Running selected normalization method: TSS
2025-09-03 21:59:53.070586 INFO::Running selected transform method: LOG
2025-09-03 21:59:53.080875 INFO::Fitting model to feature number 1, a
2025-09-03 21:59:53.086016 INFO::Fitting model to feature number 2, b
2025-09-03 21:59:53.092034 INFO::Fitting model to feature number 3, c
2025-09-03 21:59:53.202794 INFO::Creating output folder
2025-09-03 21:59:53.204388 INFO::Creating fits folder
2025-09-03 21:59:53.20586 INFO::Writing residuals to file /tmp/RtmpIBPeq6/filefc140097016/fits/residuals_linear.rds
2025-09-03 21:59:53.207179 INFO::Writing fitted values to file /tmp/RtmpIBPeq6/filefc140097016/fits/fitted_linear.rds
2025-09-03 21:59:53.208426 INFO::Writing residuals to file /tmp/RtmpIBPeq6/filefc140097016/fits/residuals_logistic.rds
2025-09-03 21:59:53.210182 INFO::Writing fitted values to file /tmp/RtmpIBPeq6/filefc140097016/fits/fitted_logistic.rds
2025-09-03 21:59:53.213452 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpIBPeq6/filefc140097016/all_results.tsv
2025-09-03 21:59:53.215217 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/RtmpIBPeq6/filefc140097016/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
349.518 7.608 359.291
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 23.767 | 1.054 | 25.064 | |
| maaslin_check_arguments | 0.154 | 0.003 | 0.159 | |
| maaslin_check_formula | 0.172 | 0.009 | 0.181 | |
| maaslin_compute_formula | 0.175 | 0.010 | 0.186 | |
| maaslin_contrast_test | 19.694 | 0.938 | 20.841 | |
| maaslin_filter | 1.423 | 0.262 | 1.701 | |
| maaslin_fit | 14.104 | 0.727 | 14.923 | |
| maaslin_log_arguments | 0.183 | 0.010 | 0.196 | |
| maaslin_normalize | 0.381 | 0.026 | 0.410 | |
| maaslin_plot_results | 41.943 | 1.057 | 43.290 | |
| maaslin_plot_results_from_output | 41.597 | 0.913 | 42.773 | |
| maaslin_process_metadata | 0.643 | 0.043 | 0.695 | |
| maaslin_read_data | 0.181 | 0.009 | 0.192 | |
| maaslin_reorder_data | 0.184 | 0.010 | 0.197 | |
| maaslin_transform | 0.793 | 0.072 | 0.873 | |
| maaslin_write_results | 16.690 | 0.864 | 17.681 | |
| maaslin_write_results_lefse_format | 16.363 | 0.546 | 16.991 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.001 | 0.006 | |