William Nickols
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 1152/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-18 22:00:53 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 22:14:56 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 842.1 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 49.713 1.072 51.233
maaslin_plot_results_from_output 49.333 1.050 50.982
maaslin3 22.630 1.066 23.949
maaslin_contrast_test 19.868 0.973 21.031
maaslin_write_results_lefse_format 17.893 0.707 18.728
maaslin_write_results 16.141 0.552 16.824
maaslin_fit 15.331 0.918 16.387
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-18 22:08:02.197571 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:08:02.314502 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:08:02.442678 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:08:02.473391 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:08:02.520018 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:08:02.629873 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:08:02.637626 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:08:02.652444 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:08:02.763237 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:08:02.769932 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:08:02.832259 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:08:02.886674 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:08:02.900974 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:08:02.949864 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:08:03.045004 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:08:20.030136 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:08:20.122929 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:08:20.219739 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:08:20.249695 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:08:20.296503 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:08:20.427754 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:08:20.435531 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:08:20.453087 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:08:20.5686 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:08:20.576474 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:08:20.632043 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:08:20.687211 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:08:20.701402 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:08:20.750729 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:08:20.845195 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:08:25.593 R[61453:33717951] XType: Using static font registry.
2025-11-18 22:08:48.433111 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:08:48.537924 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:08:48.638688 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:08:48.672601 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:08:48.724804 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:08:48.834703 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:08:48.842172 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:08:48.859491 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:08:48.999815 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:08:49.008611 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:08:49.085501 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:08:49.14614 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:08:49.163626 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:08:49.223556 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:08:49.325417 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:09:04.923956 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:09:05.026015 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:09:05.163877 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:09:05.194559 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:09:05.241308 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:09:05.345398 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:09:05.350856 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:09:05.368312 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:09:05.501885 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:09:05.510709 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:09:05.576348 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:09:05.628061 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:09:05.643572 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:09:05.708377 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:09:05.795677 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:09:06.058481 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/residuals_linear.rds
2025-11-18 22:09:06.125647 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/fitted_linear.rds
2025-11-18 22:09:06.196868 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/residuals_logistic.rds
2025-11-18 22:09:06.536145 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/fitted_logistic.rds
2025-11-18 22:09:31.679502 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:09:31.776968 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:09:31.874449 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:09:31.906016 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:09:31.950296 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:09:32.047768 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:09:32.056319 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:09:32.069992 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:09:32.194647 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:09:32.200972 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:09:32.267054 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:09:32.321804 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:09:32.337946 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:09:32.380297 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:09:32.466906 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:09:47.457523 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:09:47.576062 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:09:47.686803 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:09:47.716822 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:09:47.768515 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:09:47.879318 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:09:47.885791 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:09:47.905465 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:09:48.032845 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:09:48.040682 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:09:48.115469 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:09:48.172409 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:09:48.193685 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:09:48.254287 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:09:48.364526 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:09:48.71223 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/residuals_linear.rds
2025-11-18 22:09:48.778243 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/fitted_linear.rds
2025-11-18 22:09:48.848178 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/residuals_logistic.rds
2025-11-18 22:09:49.185942 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/fitted_logistic.rds
2025-11-18 22:10:13.304981 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:10:13.400133 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:10:13.504197 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:10:13.537849 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:10:13.58557 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:10:13.69176 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:10:13.700672 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:10:13.716889 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:10:13.8944 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:10:13.903896 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:10:13.973966 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:10:14.032583 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:10:14.049387 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:10:14.106544 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:10:14.207715 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:10:27.555479 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:10:27.651713 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:10:27.750638 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:10:27.778481 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:10:27.817837 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:10:27.916778 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:10:27.924851 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:10:27.937491 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:10:28.065513 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:10:28.072077 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:10:28.13331 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:10:28.191235 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:10:28.208709 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:10:28.256662 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:10:28.339805 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:10:28.66021 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/residuals_linear.rds
2025-11-18 22:10:28.720713 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/fitted_linear.rds
2025-11-18 22:10:28.78468 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/residuals_logistic.rds
2025-11-18 22:10:29.093791 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d1177de27/fits/fitted_logistic.rds
2025-11-18 22:10:53.942833 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:10:54.049369 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:10:54.145946 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:10:54.172934 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:10:54.214723 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:10:54.315238 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:10:54.323787 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:10:54.342824 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:10:54.457509 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:10:54.466169 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:10:54.529337 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:10:54.582611 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:10:54.595423 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:10:54.648334 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:10:54.735397 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:11:07.569205 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:11:07.655867 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:11:07.798266 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:11:07.829064 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:11:07.871058 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:11:07.959037 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:11:07.966121 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:11:07.980268 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:11:08.102561 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:11:08.108489 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:11:08.164802 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:11:08.219152 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:11:08.234219 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:11:08.285928 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:11:08.363952 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:11:36.378938 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:11:46.193792 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:12:14.355069 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:12:25.638552 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:12:26.344538 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_linear.rds
2025-11-18 22:12:26.406758 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_linear.rds
2025-11-18 22:12:26.441579 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_logistic.rds
2025-11-18 22:12:26.505344 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_logistic.rds
2025-11-18 22:12:51.783109 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:12:58.320075 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:12:58.720676 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_linear.rds
2025-11-18 22:12:58.788064 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_linear.rds
2025-11-18 22:12:58.832618 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_logistic.rds
2025-11-18 22:12:58.905426 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_logistic.rds
2025-11-18 22:13:21.519972 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:13:28.985227 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 22:13:29.387814 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_linear.rds
2025-11-18 22:13:29.456568 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_linear.rds
2025-11-18 22:13:29.500596 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_logistic.rds
2025-11-18 22:13:29.565531 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_logistic.rds
2025-11-18 22:13:49.742599 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:13:49.847029 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:13:49.941216 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:13:49.967158 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:13:50.011145 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:13:50.106566 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:13:50.113333 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:13:50.130054 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:13:50.257727 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:13:50.265397 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:13:50.370215 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:13:50.428691 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:13:50.444368 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:13:50.504996 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:13:50.593563 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:14:05.166602 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 22:14:05.262442 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 22:14:05.345264 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 22:14:05.369445 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 22:14:05.410303 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 22:14:05.503849 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 22:14:05.509892 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 22:14:05.52323 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 22:14:05.636499 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 22:14:05.6419 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 22:14:05.705705 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 22:14:05.760015 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 22:14:05.774402 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 22:14:05.822244 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 22:14:05.920091 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 22:14:06.197674 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_linear.rds
2025-11-18 22:14:06.2596 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_linear.rds
2025-11-18 22:14:06.324852 WARNING::Deleting existing residuals file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/residuals_logistic.rds
2025-11-18 22:14:06.645283 WARNING::Deleting existing fitted file: /tmp/Rtmp9idQ4v/filef00d7bf2737e/fits/fitted_logistic.rds
2025-11-18 22:14:29.974137 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-18 22:14:29.999803 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-18 22:14:30.015613 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-18 22:14:30.08329 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-18 22:14:30.099574 ERROR::Effect name not found in metadata: d
2025-11-18 22:14:30.110218 ERROR::No user formula provided
2025-11-18 22:14:30.146989 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-18 22:14:30.158725 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-18 22:14:33.676833 INFO::Writing function arguments to log file
2025-11-18 22:14:33.702087 INFO::Verifying options selected are valid
2025-11-18 22:14:36.532967 INFO::Writing function arguments to log file
2025-11-18 22:14:36.55359 INFO::Verifying options selected are valid
2025-11-18 22:14:36.554965 INFO::Determining format of input files
2025-11-18 22:14:36.556025 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 22:14:36.558611 INFO::Running selected normalization method: TSS
2025-11-18 22:14:36.560141 INFO::Creating output feature tables folder
2025-11-18 22:14:36.561314 INFO::Writing normalized data to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/features/data_norm.tsv
2025-11-18 22:14:36.563089 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-18 22:14:36.564281 INFO::Total samples in data: 16
2025-11-18 22:14:36.56582 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-18 22:14:36.567256 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-18 22:14:36.570179 INFO::Total filtered features: 0
2025-11-18 22:14:36.57171 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-18 22:14:36.573502 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-18 22:14:36.574988 INFO::Filtered feature names from variance filtering:
2025-11-18 22:14:36.575983 INFO::Writing filtered data to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/features/filtered_data.tsv
2025-11-18 22:14:36.578517 INFO::Running selected transform method: LOG
2025-11-18 22:14:36.580497 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/features/data_transformed.tsv
2025-11-18 22:14:36.583476 INFO::Applying z-score to standardize continuous metadata
2025-11-18 22:14:36.589989 INFO::Running the linear model component
2025-11-18 22:14:36.612837 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:36.617815 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:36.624666 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:36.635373 INFO::Counting total values for each feature
2025-11-18 22:14:36.63811 INFO::Running the logistic model component
2025-11-18 22:14:36.662202 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:36.66968 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:36.677105 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:36.68963 INFO::Counting total values for each feature
2025-11-18 22:14:36.692345 INFO::Re-running abundances for warn_prevalence
2025-11-18 22:14:36.694147 INFO::Running selected normalization method: TSS
2025-11-18 22:14:36.696762 INFO::Running selected transform method: LOG
2025-11-18 22:14:36.722833 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:36.728978 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:36.73545 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:36.84157 INFO::Creating fits folder
2025-11-18 22:14:36.843889 INFO::Writing residuals to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/fits/residuals_linear.rds
2025-11-18 22:14:36.845684 INFO::Writing fitted values to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/fits/fitted_linear.rds
2025-11-18 22:14:36.847226 INFO::Writing residuals to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/fits/residuals_logistic.rds
2025-11-18 22:14:36.848687 INFO::Writing fitted values to file /tmp/Rtmp9idQ4v/filef00d3c74bd9e/fits/fitted_logistic.rds
2025-11-18 22:14:36.851691 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9idQ4v/filef00d3c74bd9e/all_results.tsv
2025-11-18 22:14:36.853746 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/Rtmp9idQ4v/filef00d3c74bd9e/significant_results.tsv
2025-11-18 22:14:36.855457 INFO::Creating output figures folder
2025-11-18 22:14:36.857057 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9idQ4v/filef00d3c74bd9e/figures/summary_plot.pdf
2025-11-18 22:14:38.717145 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9idQ4v/filef00d3c74bd9e/figures
2025-11-18 22:14:38.719524 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 22:14:38.725286 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 22:14:39.311482 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp9idQ4v/filef00d3c74bd9e/figures/summary_plot.pdf
2025-11-18 22:14:41.163172 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9idQ4v/filef00d3c74bd9e/figures
2025-11-18 22:14:41.165472 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 22:14:41.169819 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 22:14:41.766849 INFO::Running the linear model component
2025-11-18 22:14:41.777348 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:41.782162 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:41.788119 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:41.795469 INFO::Counting total values for each feature
2025-11-18 22:14:41.79789 INFO::Running the logistic model component
2025-11-18 22:14:41.808899 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:41.815457 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:41.821773 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:41.832043 INFO::Counting total values for each feature
2025-11-18 22:14:41.834857 INFO::Re-running abundances for warn_prevalence
2025-11-18 22:14:41.836033 INFO::Running selected normalization method: TSS
2025-11-18 22:14:41.837928 INFO::Running selected transform method: LOG
2025-11-18 22:14:41.84966 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:41.871366 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:41.878976 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:41.991807 INFO::Creating output folder
2025-11-18 22:14:41.993096 INFO::Creating output figures folder
2025-11-18 22:14:41.994915 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9idQ4v/filef00d27fb31af/figures/summary_plot.pdf
2025-11-18 22:14:43.869647 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9idQ4v/filef00d27fb31af/figures
2025-11-18 22:14:43.871421 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 22:14:43.877001 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 22:14:45.032738 INFO::Applying z-score to standardize continuous metadata
2025-11-18 22:14:45.041292 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-18 22:14:45.042517 INFO::Bypass z-score application to metadata
2025-11-18 22:14:45.045776 INFO::Bypass z-score application to metadata
2025-11-18 22:14:45.074715 INFO::Determining format of input files
2025-11-18 22:14:45.0757 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 22:14:45.076489 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-18 22:14:45.08542 INFO::Determining format of input files
2025-11-18 22:14:45.086526 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-18 22:14:45.08815 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 22:14:45.10012 INFO::Determining format of input files
2025-11-18 22:14:45.101596 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 22:14:45.103125 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 22:14:45.105494 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-18 22:14:45.106518 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-18 22:14:45.122425 INFO::Running selected transform method: LOG
2025-11-18 22:14:45.123802 INFO::Creating output feature tables folder
2025-11-18 22:14:45.124804 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9idQ4v/filef00d6b9d75b8/features/data_transformed.tsv
2025-11-18 22:14:45.131395 INFO::Running selected transform method: LOG
2025-11-18 22:14:45.132824 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9idQ4v/filef00d6b9d75b8/features/data_transformed.tsv
2025-11-18 22:14:45.137008 INFO::Running selected transform method: PLOG
2025-11-18 22:14:45.138473 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9idQ4v/filef00d6b9d75b8/features/data_transformed.tsv
2025-11-18 22:14:45.141467 INFO::Running selected transform method: NONE
2025-11-18 22:14:45.142221 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9idQ4v/filef00d6b9d75b8/features/data_transformed.tsv
2025-11-18 22:14:45.154522 INFO::Running the linear model component
2025-11-18 22:14:45.164248 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:45.168758 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:45.17303 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:45.182206 INFO::Counting total values for each feature
2025-11-18 22:14:45.184879 INFO::Running the logistic model component
2025-11-18 22:14:45.196471 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:45.203371 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:45.209458 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:45.22144 INFO::Counting total values for each feature
2025-11-18 22:14:45.224451 INFO::Re-running abundances for warn_prevalence
2025-11-18 22:14:45.225783 INFO::Running selected normalization method: TSS
2025-11-18 22:14:45.227846 INFO::Running selected transform method: LOG
2025-11-18 22:14:45.236783 INFO::Fitting model to feature number 1, a
2025-11-18 22:14:45.242782 INFO::Fitting model to feature number 2, b
2025-11-18 22:14:45.248828 INFO::Fitting model to feature number 3, c
2025-11-18 22:14:45.343834 INFO::Creating output folder
2025-11-18 22:14:45.344972 INFO::Creating fits folder
2025-11-18 22:14:45.346072 INFO::Writing residuals to file /tmp/Rtmp9idQ4v/filef00d2e9bba3a/fits/residuals_linear.rds
2025-11-18 22:14:45.347235 INFO::Writing fitted values to file /tmp/Rtmp9idQ4v/filef00d2e9bba3a/fits/fitted_linear.rds
2025-11-18 22:14:45.348381 INFO::Writing residuals to file /tmp/Rtmp9idQ4v/filef00d2e9bba3a/fits/residuals_logistic.rds
2025-11-18 22:14:45.349542 INFO::Writing fitted values to file /tmp/Rtmp9idQ4v/filef00d2e9bba3a/fits/fitted_logistic.rds
2025-11-18 22:14:45.351958 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9idQ4v/filef00d2e9bba3a/all_results.tsv
2025-11-18 22:14:45.353801 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/Rtmp9idQ4v/filef00d2e9bba3a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
405.421 7.886 416.454
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 22.630 | 1.066 | 23.949 | |
| maaslin_check_arguments | 0.188 | 0.007 | 0.198 | |
| maaslin_check_formula | 0.190 | 0.015 | 0.207 | |
| maaslin_compute_formula | 0.226 | 0.019 | 0.252 | |
| maaslin_contrast_test | 19.868 | 0.973 | 21.031 | |
| maaslin_filter | 0.587 | 0.053 | 0.647 | |
| maaslin_fit | 15.331 | 0.918 | 16.387 | |
| maaslin_log_arguments | 0.168 | 0.012 | 0.183 | |
| maaslin_normalize | 0.368 | 0.025 | 0.396 | |
| maaslin_plot_results | 49.713 | 1.072 | 51.233 | |
| maaslin_plot_results_from_output | 49.333 | 1.050 | 50.982 | |
| maaslin_process_metadata | 0.611 | 0.041 | 0.660 | |
| maaslin_read_data | 0.159 | 0.009 | 0.170 | |
| maaslin_reorder_data | 0.164 | 0.010 | 0.175 | |
| maaslin_transform | 0.760 | 0.053 | 0.829 | |
| maaslin_write_results | 16.141 | 0.552 | 16.824 | |
| maaslin_write_results_lefse_format | 17.893 | 0.707 | 18.728 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.000 | 0.004 | |