William Nickols
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_21 |
| git_last_commit: d86be18 |
| git_last_commit_date: 2025-10-12 11:15:12 -0400 (Sun, 12 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1155/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.0.2 (landing page) William Nickols
| nebbiolo1 | 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 | OK | | ||||||||
| kunpeng2 | 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: 1.0.2 |
| 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_1.0.2.tar.gz |
| StartedAt: 2025-10-14 05:55:04 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 06:23:14 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 1690.0 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_1.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.0.2’
* 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 102.796 1.584 109.431
maaslin_plot_results_from_output 100.701 1.785 105.881
maaslin_contrast_test 42.878 1.978 47.548
maaslin3 41.072 1.684 54.448
maaslin_write_results_lefse_format 37.963 1.025 39.997
maaslin_write_results 32.486 1.043 34.430
maaslin_fit 31.475 1.118 39.831
* 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 ‘1.0.2’ ** 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 RC (2025-06-05 r88288) -- "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")
2025-10-14 06:09:22.107284 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:09:22.325322 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:09:22.575016 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:09:22.654331 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:09:22.758793 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:09:22.975659 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:09:22.990729 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:09:23.024002 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:09:23.304711 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:09:23.323295 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:09:23.472454 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:09:23.631237 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:09:23.665444 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:09:23.778162 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:09:23.975247 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:09:57.840782 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:09:58.053352 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:09:58.260503 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:09:58.318953 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:09:58.416328 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:09:58.626629 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:09:58.642701 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:09:58.675854 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:09:58.952725 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:09:58.968438 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:09:59.113482 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:09:59.221297 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:09:59.251233 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:09:59.351596 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:09:59.534353 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:10:09.708 R[55283:6565517] XType: com.apple.fonts is not accessible.
2025-10-14 06:10:09.708 R[55283:6565517] XType: XTFontStaticRegistry is enabled.
2025-10-14 06:10:55.429125 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:10:55.632996 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:10:55.832347 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:10:55.931446 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:10:56.027074 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:10:56.232672 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:10:56.247883 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:10:56.280194 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:10:56.553021 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:10:56.570851 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:10:56.719558 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:10:56.846117 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:10:56.879623 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:10:56.996476 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:10:57.196877 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:11:26.304944 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:11:26.500149 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:11:26.701955 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:11:26.756952 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:11:26.841775 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:11:27.051827 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:11:27.066971 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:11:27.094608 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:11:27.362746 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:11:27.377898 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:11:27.512757 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:11:27.621429 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:11:27.652581 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:11:27.801076 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:11:27.994133 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:11:28.480317 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/residuals_linear.rds
2025-10-14 06:11:28.583908 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/fitted_linear.rds
2025-10-14 06:11:28.695501 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/residuals_logistic.rds
2025-10-14 06:11:29.268634 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/fitted_logistic.rds
2025-10-14 06:12:17.854642 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:12:18.05872 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:12:18.262675 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:12:18.320223 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:12:18.415689 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:12:18.618765 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:12:18.63316 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:12:18.666655 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:12:18.926198 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:12:18.941842 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:12:19.076623 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:12:19.189331 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:12:19.221946 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:12:19.37191 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:12:19.63022 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:12:47.149394 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:12:47.345448 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:12:47.537214 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:12:47.593092 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:12:47.682178 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:12:47.884931 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:12:47.898413 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:12:47.928419 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:12:48.227538 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:12:48.240508 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:12:48.367214 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:12:48.470799 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:12:48.502236 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:12:48.603458 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:12:48.826554 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:12:49.409531 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/residuals_linear.rds
2025-10-14 06:12:49.516918 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/fitted_linear.rds
2025-10-14 06:12:49.626521 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/residuals_logistic.rds
2025-10-14 06:12:50.187161 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/fitted_logistic.rds
2025-10-14 06:13:39.134902 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:13:39.365465 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:13:39.658916 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:13:39.732319 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:13:39.848757 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:13:40.080655 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:13:40.095702 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:13:40.129045 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:13:40.39046 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:13:40.404508 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:13:40.542054 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:13:40.648889 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:13:40.681914 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:13:40.787239 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:13:41.004375 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:14:08.200184 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:14:08.41252 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:14:08.622129 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:14:08.68095 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:14:08.77559 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:14:08.984216 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:14:08.997569 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:14:09.030925 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:14:09.286971 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:14:09.300712 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:14:09.430496 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:14:09.537296 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:14:09.568628 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:14:09.676161 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:14:09.859187 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:14:10.426233 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/residuals_linear.rds
2025-10-14 06:14:10.553723 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/fitted_linear.rds
2025-10-14 06:14:10.669267 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/residuals_logistic.rds
2025-10-14 06:14:11.235097 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32f59e57a/fits/fitted_logistic.rds
2025-10-14 06:14:59.754549 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:14:59.954545 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:15:00.14832 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:15:00.224841 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:15:00.312516 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:15:00.505514 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:15:00.518931 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:15:00.54914 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:15:00.805072 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:15:00.818015 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:15:00.946263 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:15:01.05554 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:15:01.087568 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:15:01.193096 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:15:01.427001 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:15:27.231409 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:15:27.4329 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:15:27.632565 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:15:27.691803 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:15:27.781207 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:15:27.978634 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:15:27.993469 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:15:28.026445 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:15:28.280913 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:15:28.296252 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:15:28.429111 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:15:28.541101 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:15:28.573655 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:15:28.682673 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:15:28.876381 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:16:24.985058 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:16:44.165539 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:17:40.895356 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:18:01.378284 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:18:02.948696 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_linear.rds
2025-10-14 06:18:03.09437 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_linear.rds
2025-10-14 06:18:03.156274 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_logistic.rds
2025-10-14 06:18:03.289267 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_logistic.rds
2025-10-14 06:18:55.964594 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:19:07.011765 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:19:07.828901 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_linear.rds
2025-10-14 06:19:07.934185 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_linear.rds
2025-10-14 06:19:08.002166 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_logistic.rds
2025-10-14 06:19:08.132644 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_logistic.rds
2025-10-14 06:19:54.009186 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:20:07.346844 WARNING::Fitting problem for feature 124 returning NA
2025-10-14 06:20:08.265121 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_linear.rds
2025-10-14 06:20:08.395976 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_linear.rds
2025-10-14 06:20:08.475417 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_logistic.rds
2025-10-14 06:20:08.630707 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_logistic.rds
2025-10-14 06:20:57.292419 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:20:57.513276 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:20:57.738605 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:20:57.801394 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:20:57.900299 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:20:58.12715 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:20:58.141822 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:20:58.176269 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:20:58.449993 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:20:58.464903 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:20:58.612633 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:20:58.729552 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:20:58.765252 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:20:58.884576 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:20:59.140573 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:21:27.072328 WARNING::Fitting problem for feature 50 returning NA
2025-10-14 06:21:27.289063 WARNING::Fitting problem for feature 62 returning NA
2025-10-14 06:21:27.508072 WARNING::Fitting problem for feature 74 returning NA
2025-10-14 06:21:27.568493 WARNING::Fitting problem for feature 78 returning NA
2025-10-14 06:21:27.668485 WARNING::Fitting problem for feature 84 returning NA
2025-10-14 06:21:27.888499 WARNING::Fitting problem for feature 96 returning NA
2025-10-14 06:21:27.904482 WARNING::Fitting problem for feature 97 returning NA
2025-10-14 06:21:27.94238 WARNING::Fitting problem for feature 99 returning NA
2025-10-14 06:21:28.219677 WARNING::Fitting problem for feature 114 returning NA
2025-10-14 06:21:28.236095 WARNING::Fitting problem for feature 115 returning NA
2025-10-14 06:21:28.379372 WARNING::Fitting problem for feature 123 returning NA
2025-10-14 06:21:28.497078 WARNING::Fitting problem for feature 130 returning NA
2025-10-14 06:21:28.531641 WARNING::Fitting problem for feature 132 returning NA
2025-10-14 06:21:28.647486 WARNING::Fitting problem for feature 139 returning NA
2025-10-14 06:21:28.851865 WARNING::Fitting problem for feature 150 returning NA
2025-10-14 06:21:29.634957 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_linear.rds
2025-10-14 06:21:29.74739 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_linear.rds
2025-10-14 06:21:29.867941 WARNING::Deleting existing residuals file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/residuals_logistic.rds
2025-10-14 06:21:30.512815 WARNING::Deleting existing fitted file: /tmp/RtmpigmEEM/filed7f32abf900c/fits/fitted_logistic.rds
2025-10-14 06:22:20.761626 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-14 06:22:20.812508 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-14 06:22:20.84922 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-14 06:22:21.027689 ERROR::No fixed, group, or
ordered effects included in formula.
2025-10-14 06:22:21.075119 ERROR::Effect name not found in metadata: d
2025-10-14 06:22:21.11151 ERROR::No user formula provided
2025-10-14 06:22:21.195463 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-14 06:22:21.23194 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-10-14 06:22:31.877615 INFO::Writing function arguments to log file
2025-10-14 06:22:31.926785 INFO::Verifying options selected are valid
2025-10-14 06:22:37.915539 INFO::Writing function arguments to log file
2025-10-14 06:22:37.952286 INFO::Verifying options selected are valid
2025-10-14 06:22:37.954942 INFO::Determining format of input files
2025-10-14 06:22:37.957764 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 06:22:37.963575 INFO::Running selected normalization method: TSS
2025-10-14 06:22:37.967193 INFO::Creating output feature tables folder
2025-10-14 06:22:37.970276 INFO::Writing normalized data to file /tmp/RtmpigmEEM/filed7f33c02d360/features/data_norm.tsv
2025-10-14 06:22:37.974355 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-14 06:22:37.976839 INFO::Total samples in data: 16
2025-10-14 06:22:37.979175 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-14 06:22:37.981488 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-14 06:22:37.986718 INFO::Total filtered features: 0
2025-10-14 06:22:37.989424 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-14 06:22:37.992861 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-14 06:22:37.99586 INFO::Filtered feature names from variance filtering:
2025-10-14 06:22:37.998419 INFO::Writing filtered data to file /tmp/RtmpigmEEM/filed7f33c02d360/features/filtered_data.tsv
2025-10-14 06:22:38.002402 INFO::Running selected transform method: LOG
2025-10-14 06:22:38.005583 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpigmEEM/filed7f33c02d360/features/data_transformed.tsv
2025-10-14 06:22:38.010141 INFO::Applying z-score to standardize continuous metadata
2025-10-14 06:22:38.022405 INFO::Running the linear model component
2025-10-14 06:22:38.106603 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:38.119265 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:38.132112 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:38.152655 INFO::Counting total values for each feature
2025-10-14 06:22:38.15742 INFO::Running the logistic model component
2025-10-14 06:22:38.199873 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:38.217234 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:38.233838 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:38.257706 INFO::Counting total values for each feature
2025-10-14 06:22:38.263265 INFO::Re-running abundances for warn_prevalence
2025-10-14 06:22:38.267023 INFO::Running selected normalization method: TSS
2025-10-14 06:22:38.270997 INFO::Running selected transform method: LOG
2025-10-14 06:22:38.318611 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:38.331873 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:38.343153 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:38.567836 INFO::Creating fits folder
2025-10-14 06:22:38.571002 INFO::Writing residuals to file /tmp/RtmpigmEEM/filed7f33c02d360/fits/residuals_linear.rds
2025-10-14 06:22:38.574328 INFO::Writing fitted values to file /tmp/RtmpigmEEM/filed7f33c02d360/fits/fitted_linear.rds
2025-10-14 06:22:38.57792 INFO::Writing residuals to file /tmp/RtmpigmEEM/filed7f33c02d360/fits/residuals_logistic.rds
2025-10-14 06:22:38.581259 INFO::Writing fitted values to file /tmp/RtmpigmEEM/filed7f33c02d360/fits/fitted_logistic.rds
2025-10-14 06:22:38.589178 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpigmEEM/filed7f33c02d360/all_results.tsv
2025-10-14 06:22:38.594545 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/RtmpigmEEM/filed7f33c02d360/significant_results.tsv
2025-10-14 06:22:38.599229 INFO::Creating output figures folder
2025-10-14 06:22:38.603517 INFO::Writing summary plot of significant
results to file: /tmp/RtmpigmEEM/filed7f33c02d360/figures/summary_plot.pdf
2025-10-14 06:22:42.717547 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpigmEEM/filed7f33c02d360/figures
2025-10-14 06:22:42.721876 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 06:22:42.737471 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 06:22:44.165063 INFO::Writing summary plot of
significant results to file: /tmp/RtmpigmEEM/filed7f33c02d360/figures/summary_plot.pdf
2025-10-14 06:22:48.81901 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpigmEEM/filed7f33c02d360/figures
2025-10-14 06:22:48.822702 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 06:22:48.836347 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 06:22:50.294578 INFO::Running the linear model component
2025-10-14 06:22:50.321494 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:50.33382 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:50.348105 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:50.370457 INFO::Counting total values for each feature
2025-10-14 06:22:50.374924 INFO::Running the logistic model component
2025-10-14 06:22:50.403105 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:50.418576 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:50.435672 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:50.463091 INFO::Counting total values for each feature
2025-10-14 06:22:50.468082 INFO::Re-running abundances for warn_prevalence
2025-10-14 06:22:50.47225 INFO::Running selected normalization method: TSS
2025-10-14 06:22:50.47564 INFO::Running selected transform method: LOG
2025-10-14 06:22:50.500661 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:50.511683 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:50.524827 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:50.784065 INFO::Creating output folder
2025-10-14 06:22:50.786586 INFO::Creating output figures folder
2025-10-14 06:22:50.792035 INFO::Writing summary plot of significant
results to file: /tmp/RtmpigmEEM/filed7f3b61e7fc/figures/summary_plot.pdf
2025-10-14 06:22:55.260684 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpigmEEM/filed7f3b61e7fc/figures
2025-10-14 06:22:55.264188 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-14 06:22:55.27659 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-14 06:22:57.889086 INFO::Applying z-score to standardize continuous metadata
2025-10-14 06:22:57.907305 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-14 06:22:57.909363 INFO::Bypass z-score application to metadata
2025-10-14 06:22:57.916355 INFO::Bypass z-score application to metadata
2025-10-14 06:22:57.965715 INFO::Determining format of input files
2025-10-14 06:22:57.967853 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 06:22:57.971257 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-14 06:22:57.989057 INFO::Determining format of input files
2025-10-14 06:22:57.992129 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-14 06:22:57.995353 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 06:22:58.01472 INFO::Determining format of input files
2025-10-14 06:22:58.017137 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-14 06:22:58.019807 INFO::Input format is feature_specific_covariate samples as columns
2025-10-14 06:22:58.024555 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-14 06:22:58.026675 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-14 06:22:58.055182 INFO::Running selected transform method: LOG
2025-10-14 06:22:58.057908 INFO::Creating output feature tables folder
2025-10-14 06:22:58.060535 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpigmEEM/filed7f34b98b7f1/features/data_transformed.tsv
2025-10-14 06:22:58.073057 INFO::Running selected transform method: LOG
2025-10-14 06:22:58.075797 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpigmEEM/filed7f34b98b7f1/features/data_transformed.tsv
2025-10-14 06:22:58.084683 INFO::Running selected transform method: PLOG
2025-10-14 06:22:58.089997 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpigmEEM/filed7f34b98b7f1/features/data_transformed.tsv
2025-10-14 06:22:58.097137 INFO::Running selected transform method: NONE
2025-10-14 06:22:58.099825 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpigmEEM/filed7f34b98b7f1/features/data_transformed.tsv
2025-10-14 06:22:58.118862 INFO::Running the linear model component
2025-10-14 06:22:58.14193 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:58.153109 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:58.164955 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:58.183768 INFO::Counting total values for each feature
2025-10-14 06:22:58.1878 INFO::Running the logistic model component
2025-10-14 06:22:58.210476 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:58.227048 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:58.242653 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:58.265069 INFO::Counting total values for each feature
2025-10-14 06:22:58.270161 INFO::Re-running abundances for warn_prevalence
2025-10-14 06:22:58.272224 INFO::Running selected normalization method: TSS
2025-10-14 06:22:58.2758 INFO::Running selected transform method: LOG
2025-10-14 06:22:58.300305 INFO::Fitting model to feature number 1, a
2025-10-14 06:22:58.312719 INFO::Fitting model to feature number 2, b
2025-10-14 06:22:58.324451 INFO::Fitting model to feature number 3, c
2025-10-14 06:22:58.588478 INFO::Creating output folder
2025-10-14 06:22:58.591073 INFO::Creating fits folder
2025-10-14 06:22:58.596171 INFO::Writing residuals to file /tmp/RtmpigmEEM/filed7f3175455fd/fits/residuals_linear.rds
2025-10-14 06:22:58.599329 INFO::Writing fitted values to file /tmp/RtmpigmEEM/filed7f3175455fd/fits/fitted_linear.rds
2025-10-14 06:22:58.602333 INFO::Writing residuals to file /tmp/RtmpigmEEM/filed7f3175455fd/fits/residuals_logistic.rds
2025-10-14 06:22:58.605669 INFO::Writing fitted values to file /tmp/RtmpigmEEM/filed7f3175455fd/fits/fitted_logistic.rds
2025-10-14 06:22:58.613626 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpigmEEM/filed7f3175455fd/all_results.tsv
2025-10-14 06:22:58.618916 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/RtmpigmEEM/filed7f3175455fd/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
800.656 12.238 840.183
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 41.072 | 1.684 | 54.448 | |
| maaslin_check_arguments | 0.283 | 0.008 | 0.343 | |
| maaslin_check_formula | 0.301 | 0.015 | 0.327 | |
| maaslin_compute_formula | 0.310 | 0.015 | 0.347 | |
| maaslin_contrast_test | 42.878 | 1.978 | 47.548 | |
| maaslin_filter | 1.243 | 0.115 | 2.141 | |
| maaslin_fit | 31.475 | 1.118 | 39.831 | |
| maaslin_log_arguments | 0.290 | 0.019 | 0.417 | |
| maaslin_normalize | 0.710 | 0.052 | 0.974 | |
| maaslin_plot_results | 102.796 | 1.584 | 109.431 | |
| maaslin_plot_results_from_output | 100.701 | 1.785 | 105.881 | |
| maaslin_process_metadata | 1.288 | 0.075 | 1.409 | |
| maaslin_read_data | 0.294 | 0.014 | 0.311 | |
| maaslin_reorder_data | 0.308 | 0.015 | 0.358 | |
| maaslin_transform | 1.608 | 0.105 | 1.796 | |
| maaslin_write_results | 32.486 | 1.043 | 34.430 | |
| maaslin_write_results_lefse_format | 37.963 | 1.025 | 39.997 | |
| preprocess_dna_mtx | 0.008 | 0.001 | 0.009 | |
| preprocess_taxa_mtx | 0.010 | 0.001 | 0.010 | |