William Nickols
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 2025) |
| 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:04 -0500 (Thu, 27 Nov 2025).
| 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" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | NA | |||||||||
| 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: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-11-26 11:21:48 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 11:45:56 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 1447.6 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
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 ‘1.2.0’
* 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 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 56.190 1.514 90.180
maaslin_plot_results 54.866 1.295 86.537
maaslin3 26.166 1.081 41.950
maaslin_contrast_test 23.646 1.235 37.808
maaslin_write_results 18.904 0.790 31.008
maaslin_fit 18.060 1.040 29.205
maaslin_write_results_lefse_format 16.318 0.632 26.494
* 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-arm64/Resources/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 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-11-26 11:33:38.092364 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:33:39.659792 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:33:39.819213 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:33:39.879355 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:33:39.918488 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:33:40.086343 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:33:40.098104 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:33:40.123592 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:33:40.267821 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:33:40.274711 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:33:40.464392 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:33:40.53169 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:33:40.557754 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:33:40.632058 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:33:40.804783 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:34:13.136553 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:34:13.32853 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:34:13.490736 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:34:13.536926 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:34:13.603795 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:34:13.769925 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:34:13.778045 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:34:13.799929 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:34:14.032665 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:34:14.039605 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:34:14.204471 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:34:14.325683 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:34:14.340704 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:34:14.412598 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:34:14.539493 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:34:22.344 R[70827:93498546] XType: Using static font registry.
2025-11-26 11:35:02.230235 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:35:02.39641 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:35:02.536532 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:35:02.564767 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:35:02.643813 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:35:02.822763 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:35:02.83634 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:35:02.850582 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:35:04.94973 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:35:04.961858 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:35:05.053063 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:35:05.126768 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:35:05.164362 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:35:05.221177 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:35:05.345323 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:35:30.773861 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:35:30.912485 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:35:31.046141 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:35:31.078412 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:35:31.17037 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:35:31.356102 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:35:31.365158 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:35:31.396589 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:35:31.591158 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:35:31.615214 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:35:31.715259 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:35:31.7887 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:35:31.803541 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:35:31.895535 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:35:32.031825 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:35:32.543737 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/residuals_linear.rds
2025-11-26 11:35:32.694263 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/fitted_linear.rds
2025-11-26 11:35:32.825366 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/residuals_logistic.rds
2025-11-26 11:35:33.644553 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/fitted_logistic.rds
2025-11-26 11:36:16.694138 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:36:16.852971 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:36:17.023593 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:36:17.077237 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:36:17.149748 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:36:17.321395 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:36:17.329251 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:36:17.345526 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:36:17.52022 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:36:17.526978 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:36:17.643825 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:36:17.732007 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:36:17.765529 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:36:17.850416 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:36:17.971012 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:36:43.566031 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:36:43.663772 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:36:43.933323 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:36:43.959765 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:36:44.041726 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:36:44.187631 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:36:44.194226 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:36:44.207853 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:36:44.408458 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:36:44.432654 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:36:44.541617 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:36:44.603055 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:36:44.633613 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:36:44.737209 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:36:44.915315 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:36:45.267482 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/residuals_linear.rds
2025-11-26 11:36:45.440655 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/fitted_linear.rds
2025-11-26 11:36:45.627102 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/residuals_logistic.rds
2025-11-26 11:36:46.399576 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/fitted_logistic.rds
2025-11-26 11:37:28.905279 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:37:29.101331 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:37:29.226165 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:37:29.268875 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:37:29.337821 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:37:29.508415 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:37:29.518961 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:37:29.53966 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:37:29.745469 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:37:29.752386 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:37:29.878899 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:37:29.961081 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:37:29.985381 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:37:30.047508 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:37:30.146141 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:37:53.466169 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:37:53.618929 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:37:53.779155 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:37:53.814703 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:37:53.877841 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:37:54.022318 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:37:54.029322 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:37:54.064473 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:37:54.211826 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:37:54.218819 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:37:54.304673 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:37:54.356196 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:37:54.425222 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:37:54.519199 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:37:54.648981 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:37:55.172535 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/residuals_linear.rds
2025-11-26 11:37:55.327363 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/fitted_linear.rds
2025-11-26 11:37:55.486183 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/residuals_logistic.rds
2025-11-26 11:37:56.304898 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab6e29f2f3/fits/fitted_logistic.rds
2025-11-26 11:38:38.922245 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:38:39.122392 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:38:39.302884 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:38:39.348683 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:38:39.408931 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:38:39.569412 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:38:39.575928 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:38:39.589635 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:38:39.701634 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:38:39.708739 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:38:39.767181 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:38:39.882285 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:38:39.934863 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:38:40.016876 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:38:40.157487 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:39:05.228166 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:39:05.369233 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:39:05.514921 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:39:05.543815 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:39:05.613924 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:39:05.752136 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:39:05.759757 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:39:05.774693 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:39:05.951599 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:39:05.973311 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:39:06.062706 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:39:06.128413 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:39:06.153561 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:39:06.235509 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:39:06.366938 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:39:57.596585 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:40:14.909655 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:41:07.507946 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:41:27.42189 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:41:28.402842 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_linear.rds
2025-11-26 11:41:28.574523 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_linear.rds
2025-11-26 11:41:28.67961 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_logistic.rds
2025-11-26 11:41:28.84187 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_logistic.rds
2025-11-26 11:42:15.258205 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:42:24.690982 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:42:25.277322 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_linear.rds
2025-11-26 11:42:25.403758 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_linear.rds
2025-11-26 11:42:25.48948 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_logistic.rds
2025-11-26 11:42:25.643603 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_logistic.rds
2025-11-26 11:43:03.165871 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:43:15.993861 WARNING::Fitting problem for feature 124 returning NA
2025-11-26 11:43:16.639723 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_linear.rds
2025-11-26 11:43:16.770994 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_linear.rds
2025-11-26 11:43:16.87912 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_logistic.rds
2025-11-26 11:43:17.163067 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_logistic.rds
2025-11-26 11:43:54.092939 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:43:54.307484 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:43:54.444315 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:43:54.497667 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:43:54.554334 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:43:54.680181 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:43:54.696196 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:43:54.710729 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:43:54.951254 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:43:54.964072 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:43:55.065529 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:43:55.143506 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:43:55.159265 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:43:55.232094 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:43:55.352437 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:44:20.459254 WARNING::Fitting problem for feature 50 returning NA
2025-11-26 11:44:20.628401 WARNING::Fitting problem for feature 62 returning NA
2025-11-26 11:44:20.790275 WARNING::Fitting problem for feature 74 returning NA
2025-11-26 11:44:20.862676 WARNING::Fitting problem for feature 78 returning NA
2025-11-26 11:44:20.915095 WARNING::Fitting problem for feature 84 returning NA
2025-11-26 11:44:21.060872 WARNING::Fitting problem for feature 96 returning NA
2025-11-26 11:44:21.072166 WARNING::Fitting problem for feature 97 returning NA
2025-11-26 11:44:21.086568 WARNING::Fitting problem for feature 99 returning NA
2025-11-26 11:44:21.310931 WARNING::Fitting problem for feature 114 returning NA
2025-11-26 11:44:21.317358 WARNING::Fitting problem for feature 115 returning NA
2025-11-26 11:44:21.38541 WARNING::Fitting problem for feature 123 returning NA
2025-11-26 11:44:21.461479 WARNING::Fitting problem for feature 130 returning NA
2025-11-26 11:44:21.478367 WARNING::Fitting problem for feature 132 returning NA
2025-11-26 11:44:21.572989 WARNING::Fitting problem for feature 139 returning NA
2025-11-26 11:44:21.718338 WARNING::Fitting problem for feature 150 returning NA
2025-11-26 11:44:22.261989 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_linear.rds
2025-11-26 11:44:22.490856 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_linear.rds
2025-11-26 11:44:22.679258 WARNING::Deleting existing residuals file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/residuals_logistic.rds
2025-11-26 11:44:23.499533 WARNING::Deleting existing fitted file: /tmp/Rtmp47r0ft/file114ab7faaf7c8/fits/fitted_logistic.rds
2025-11-26 11:45:07.862481 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-26 11:45:07.882207 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-26 11:45:07.894798 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-26 11:45:08.037955 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-26 11:45:08.062689 ERROR::Effect name not found in metadata: d
2025-11-26 11:45:08.102124 ERROR::No user formula provided
2025-11-26 11:45:08.174428 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-26 11:45:08.211816 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-26 11:45:14.009186 INFO::Writing function arguments to log file
2025-11-26 11:45:14.029514 INFO::Verifying options selected are valid
2025-11-26 11:45:19.274674 INFO::Writing function arguments to log file
2025-11-26 11:45:19.294662 INFO::Verifying options selected are valid
2025-11-26 11:45:19.296 INFO::Determining format of input files
2025-11-26 11:45:19.297028 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-26 11:45:19.299568 INFO::Running selected normalization method: TSS
2025-11-26 11:45:19.301273 INFO::Creating output feature tables folder
2025-11-26 11:45:19.302496 INFO::Writing normalized data to file /tmp/Rtmp47r0ft/file114ab423fb6b1/features/data_norm.tsv
2025-11-26 11:45:19.304404 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-26 11:45:19.305359 INFO::Total samples in data: 16
2025-11-26 11:45:19.306221 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-26 11:45:19.307081 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-26 11:45:19.309106 INFO::Total filtered features: 0
2025-11-26 11:45:19.310317 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-26 11:45:19.311596 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-26 11:45:19.312611 INFO::Filtered feature names from variance filtering:
2025-11-26 11:45:19.313583 INFO::Writing filtered data to file /tmp/Rtmp47r0ft/file114ab423fb6b1/features/filtered_data.tsv
2025-11-26 11:45:19.315424 INFO::Running selected transform method: LOG
2025-11-26 11:45:19.316673 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp47r0ft/file114ab423fb6b1/features/data_transformed.tsv
2025-11-26 11:45:19.318602 INFO::Applying z-score to standardize continuous metadata
2025-11-26 11:45:19.324427 INFO::Running the linear model component
2025-11-26 11:45:19.364854 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:19.370469 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:19.375202 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:19.403951 INFO::Counting total values for each feature
2025-11-26 11:45:19.406764 INFO::Running the logistic model component
2025-11-26 11:45:19.436583 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:19.454867 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:19.49262 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:19.51314 INFO::Counting total values for each feature
2025-11-26 11:45:19.516016 INFO::Re-running abundances for warn_prevalence
2025-11-26 11:45:19.51715 INFO::Running selected normalization method: TSS
2025-11-26 11:45:19.518816 INFO::Running selected transform method: LOG
2025-11-26 11:45:19.536276 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:19.553432 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:19.558795 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:19.743383 INFO::Creating fits folder
2025-11-26 11:45:19.745416 INFO::Writing residuals to file /tmp/Rtmp47r0ft/file114ab423fb6b1/fits/residuals_linear.rds
2025-11-26 11:45:19.747081 INFO::Writing fitted values to file /tmp/Rtmp47r0ft/file114ab423fb6b1/fits/fitted_linear.rds
2025-11-26 11:45:19.748577 INFO::Writing residuals to file /tmp/Rtmp47r0ft/file114ab423fb6b1/fits/residuals_logistic.rds
2025-11-26 11:45:19.760387 INFO::Writing fitted values to file /tmp/Rtmp47r0ft/file114ab423fb6b1/fits/fitted_logistic.rds
2025-11-26 11:45:19.764063 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp47r0ft/file114ab423fb6b1/all_results.tsv
2025-11-26 11:45:19.773589 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/Rtmp47r0ft/file114ab423fb6b1/significant_results.tsv
2025-11-26 11:45:19.775808 INFO::Creating output figures folder
2025-11-26 11:45:19.777625 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp47r0ft/file114ab423fb6b1/figures/summary_plot.pdf
2025-11-26 11:45:23.329863 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp47r0ft/file114ab423fb6b1/figures
2025-11-26 11:45:23.332664 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-26 11:45:23.352978 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-26 11:45:24.494254 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp47r0ft/file114ab423fb6b1/figures/summary_plot.pdf
2025-11-26 11:45:32.049992 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp47r0ft/file114ab423fb6b1/figures
2025-11-26 11:45:32.051758 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-26 11:45:32.065038 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-26 11:45:33.008542 INFO::Running the linear model component
2025-11-26 11:45:33.02625 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:33.031348 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:33.037789 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:33.046929 INFO::Counting total values for each feature
2025-11-26 11:45:33.048903 INFO::Running the logistic model component
2025-11-26 11:45:33.064969 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:33.072683 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:33.079084 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:33.092926 INFO::Counting total values for each feature
2025-11-26 11:45:33.099319 INFO::Re-running abundances for warn_prevalence
2025-11-26 11:45:33.100922 INFO::Running selected normalization method: TSS
2025-11-26 11:45:33.102546 INFO::Running selected transform method: LOG
2025-11-26 11:45:33.126545 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:33.131525 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:33.135646 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:33.294749 INFO::Creating output folder
2025-11-26 11:45:33.29624 INFO::Creating output figures folder
2025-11-26 11:45:33.297741 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp47r0ft/file114ab2156a19b/figures/summary_plot.pdf
2025-11-26 11:45:36.537509 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp47r0ft/file114ab2156a19b/figures
2025-11-26 11:45:36.543916 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-26 11:45:36.555913 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-26 11:45:38.639538 INFO::Applying z-score to standardize continuous metadata
2025-11-26 11:45:38.6495 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-26 11:45:38.650492 INFO::Bypass z-score application to metadata
2025-11-26 11:45:38.653337 INFO::Bypass z-score application to metadata
2025-11-26 11:45:38.776349 INFO::Determining format of input files
2025-11-26 11:45:38.780805 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-26 11:45:38.781811 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-26 11:45:38.792152 INFO::Determining format of input files
2025-11-26 11:45:38.793491 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-26 11:45:38.794663 INFO::Input format is feature_specific_covariate samples as columns
2025-11-26 11:45:38.809531 INFO::Determining format of input files
2025-11-26 11:45:38.810746 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-26 11:45:38.811747 INFO::Input format is feature_specific_covariate samples as columns
2025-11-26 11:45:38.813218 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-26 11:45:38.813893 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-26 11:45:38.826002 INFO::Running selected transform method: LOG
2025-11-26 11:45:38.836143 INFO::Creating output feature tables folder
2025-11-26 11:45:38.837609 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp47r0ft/file114ab3600f077/features/data_transformed.tsv
2025-11-26 11:45:38.844117 INFO::Running selected transform method: LOG
2025-11-26 11:45:38.845373 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp47r0ft/file114ab3600f077/features/data_transformed.tsv
2025-11-26 11:45:38.849454 INFO::Running selected transform method: PLOG
2025-11-26 11:45:38.850997 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp47r0ft/file114ab3600f077/features/data_transformed.tsv
2025-11-26 11:45:38.853994 INFO::Running selected transform method: NONE
2025-11-26 11:45:38.854746 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp47r0ft/file114ab3600f077/features/data_transformed.tsv
2025-11-26 11:45:38.870557 INFO::Running the linear model component
2025-11-26 11:45:38.88426 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:38.889534 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:38.90279 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:38.913045 INFO::Counting total values for each feature
2025-11-26 11:45:38.914952 INFO::Running the logistic model component
2025-11-26 11:45:38.922711 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:38.928977 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:38.948929 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:38.967145 INFO::Counting total values for each feature
2025-11-26 11:45:38.969546 INFO::Re-running abundances for warn_prevalence
2025-11-26 11:45:38.970312 INFO::Running selected normalization method: TSS
2025-11-26 11:45:38.972666 INFO::Running selected transform method: LOG
2025-11-26 11:45:38.981825 INFO::Fitting model to feature number 1, a
2025-11-26 11:45:38.989744 INFO::Fitting model to feature number 2, b
2025-11-26 11:45:38.996328 INFO::Fitting model to feature number 3, c
2025-11-26 11:45:39.130797 INFO::Creating output folder
2025-11-26 11:45:39.132135 INFO::Creating fits folder
2025-11-26 11:45:39.132991 INFO::Writing residuals to file /tmp/Rtmp47r0ft/file114ab77ab3053/fits/residuals_linear.rds
2025-11-26 11:45:39.13447 INFO::Writing fitted values to file /tmp/Rtmp47r0ft/file114ab77ab3053/fits/fitted_linear.rds
2025-11-26 11:45:39.135512 INFO::Writing residuals to file /tmp/Rtmp47r0ft/file114ab77ab3053/fits/residuals_logistic.rds
2025-11-26 11:45:39.136567 INFO::Writing fitted values to file /tmp/Rtmp47r0ft/file114ab77ab3053/fits/fitted_logistic.rds
2025-11-26 11:45:39.145516 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp47r0ft/file114ab77ab3053/all_results.tsv
2025-11-26 11:45:39.14852 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/Rtmp47r0ft/file114ab77ab3053/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
461.123 10.141 741.988
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 26.166 | 1.081 | 41.950 | |
| maaslin_check_arguments | 0.229 | 0.005 | 0.337 | |
| maaslin_check_formula | 0.203 | 0.011 | 0.310 | |
| maaslin_compute_formula | 0.207 | 0.010 | 0.316 | |
| maaslin_contrast_test | 23.646 | 1.235 | 37.808 | |
| maaslin_filter | 0.718 | 0.060 | 1.289 | |
| maaslin_fit | 18.060 | 1.040 | 29.205 | |
| maaslin_log_arguments | 0.199 | 0.010 | 0.357 | |
| maaslin_normalize | 0.407 | 0.033 | 0.666 | |
| maaslin_plot_results | 54.866 | 1.295 | 86.537 | |
| maaslin_plot_results_from_output | 56.190 | 1.514 | 90.180 | |
| maaslin_process_metadata | 0.732 | 0.054 | 1.131 | |
| maaslin_read_data | 0.181 | 0.009 | 0.287 | |
| maaslin_reorder_data | 0.189 | 0.011 | 0.309 | |
| maaslin_transform | 0.915 | 0.070 | 1.527 | |
| maaslin_write_results | 18.904 | 0.790 | 31.008 | |
| maaslin_write_results_lefse_format | 16.318 | 0.632 | 26.494 | |
| preprocess_dna_mtx | 0.004 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.001 | 0.005 | |