William Nickols
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 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 2025-11-24 12:06 -0500 (Mon, 24 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" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| 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 | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.2.0 |
| 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: 2025-11-22 09:41:06 -0500 (Sat, 22 Nov 2025) |
| EndedAt: 2025-11-22 10:02:44 -0500 (Sat, 22 Nov 2025) |
| EllapsedTime: 1297.8 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 55.468 1.236 79.153
maaslin_plot_results 54.416 1.332 77.493
maaslin3 25.845 1.092 36.788
maaslin_contrast_test 23.747 1.337 34.284
maaslin_write_results_lefse_format 19.060 0.880 28.458
maaslin_write_results 17.516 0.629 25.471
maaslin_fit 16.952 1.118 24.830
* 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")
2025-11-22 09:51:44.901571 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:51:46.259968 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:51:46.404708 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:51:46.442991 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:51:46.504346 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:51:46.660206 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:51:46.667111 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:51:46.684776 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:51:46.827666 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:51:46.838819 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:51:46.928529 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:51:46.986224 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:51:47.02328 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:51:47.083794 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:51:47.218574 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:52:16.31661 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:52:16.466268 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:52:16.629511 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:52:16.700641 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:52:16.758888 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:52:16.900976 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:52:16.910907 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:52:16.928007 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:52:17.150138 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:52:17.157699 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:52:17.249807 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:52:17.299304 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:52:17.312441 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:52:17.355239 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:52:17.525996 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:52:24.237 R[98730:50995958] XType: Using static font registry.
2025-11-22 09:52:59.740227 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:52:59.902363 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:53:00.0724 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:53:00.099174 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:53:00.141144 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:53:00.327756 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:53:00.342584 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:53:00.377303 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:53:02.566807 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:53:02.573591 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:53:02.674634 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:53:02.766585 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:53:02.788969 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:53:02.848373 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:53:02.988159 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:53:25.963023 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:53:26.091532 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:53:26.227753 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:53:26.259469 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:53:26.318419 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:53:26.506175 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:53:26.515504 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:53:26.572453 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:53:26.806849 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:53:26.824204 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:53:26.917921 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:53:26.997762 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:53:27.027264 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:53:27.123623 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:53:27.257899 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:53:27.611514 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/residuals_linear.rds
2025-11-22 09:53:27.719302 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/fitted_linear.rds
2025-11-22 09:53:27.852453 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/residuals_logistic.rds
2025-11-22 09:53:28.669339 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/fitted_logistic.rds
2025-11-22 09:54:05.650651 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:54:05.779405 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:54:05.927237 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:54:05.967744 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:54:06.037782 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:54:06.187396 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:54:06.200146 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:54:06.237247 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:54:06.404367 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:54:06.414363 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:54:06.491092 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:54:06.557196 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:54:06.577422 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:54:06.645082 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:54:06.734556 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:54:30.080522 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:54:30.295339 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:54:30.422589 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:54:30.468555 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:54:30.554026 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:54:30.68358 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:54:30.690519 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:54:30.710851 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:54:30.919459 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:54:30.926179 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:54:31.010611 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:54:31.116072 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:54:31.142783 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:54:31.23263 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:54:31.368822 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:54:31.825042 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/residuals_linear.rds
2025-11-22 09:54:31.966014 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/fitted_linear.rds
2025-11-22 09:54:32.137981 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/residuals_logistic.rds
2025-11-22 09:54:32.943561 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/fitted_logistic.rds
2025-11-22 09:55:10.743412 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:55:10.852545 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:55:11.023935 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:55:11.06347 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:55:11.137509 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:55:11.260284 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:55:11.272784 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:55:11.300533 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:55:11.482989 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:55:11.490446 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:55:11.594905 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:55:11.698209 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:55:11.722601 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:55:11.796055 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:55:11.938165 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:55:32.735652 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:55:32.8578 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:55:33.015839 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:55:33.050758 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:55:33.108301 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:55:33.253843 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:55:33.272022 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:55:33.298854 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:55:33.500911 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:55:33.511035 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:55:33.594295 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:55:33.653216 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:55:33.666991 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:55:33.752829 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:55:33.900789 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:55:34.30092 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/residuals_linear.rds
2025-11-22 09:55:34.441138 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/fitted_linear.rds
2025-11-22 09:55:34.558392 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/residuals_logistic.rds
2025-11-22 09:55:35.239749 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa5ce93925/fits/fitted_logistic.rds
2025-11-22 09:56:13.442825 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:56:13.573617 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:56:13.802934 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:56:13.925529 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:56:13.979044 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:56:14.107326 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:56:14.12224 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:56:14.136741 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:56:14.341132 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:56:14.348588 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:56:14.438812 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:56:14.516008 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:56:14.530569 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:56:14.612367 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:56:14.746657 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:56:35.596978 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 09:56:35.747903 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 09:56:35.942116 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 09:56:35.969323 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 09:56:36.041224 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 09:56:36.19921 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 09:56:36.208373 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 09:56:36.223319 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 09:56:36.416206 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 09:56:36.424597 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 09:56:36.509766 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 09:56:36.557379 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 09:56:36.572441 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 09:56:36.627006 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 09:56:36.7644 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 09:57:22.988886 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 09:57:38.16356 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 09:58:26.400464 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 09:58:45.268088 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 09:58:46.325195 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_linear.rds
2025-11-22 09:58:46.460218 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_linear.rds
2025-11-22 09:58:46.554538 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_logistic.rds
2025-11-22 09:58:46.700215 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_logistic.rds
2025-11-22 09:59:28.205166 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 09:59:37.012424 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 09:59:37.529432 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_linear.rds
2025-11-22 09:59:37.660646 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_linear.rds
2025-11-22 09:59:37.755971 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_logistic.rds
2025-11-22 09:59:37.957978 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_logistic.rds
2025-11-22 10:00:11.492725 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 10:00:23.196849 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 10:00:23.772217 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_linear.rds
2025-11-22 10:00:23.906014 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_linear.rds
2025-11-22 10:00:24.015452 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_logistic.rds
2025-11-22 10:00:24.15889 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_logistic.rds
2025-11-22 10:00:56.899884 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 10:00:57.067739 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 10:00:57.19056 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 10:00:57.224554 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 10:00:57.296592 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 10:00:57.42782 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 10:00:57.441015 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 10:00:57.456079 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 10:00:57.656689 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 10:00:57.6635 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 10:00:57.729244 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 10:00:57.785872 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 10:00:57.80397 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 10:00:57.886653 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 10:00:57.96805 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 10:01:19.133228 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 10:01:19.238193 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 10:01:19.383683 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 10:01:19.413302 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 10:01:19.450387 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 10:01:19.559631 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 10:01:19.572446 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 10:01:19.605699 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 10:01:19.776855 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 10:01:19.785263 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 10:01:19.874825 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 10:01:19.932126 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 10:01:19.953449 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 10:01:20.025212 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 10:01:20.255433 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 10:01:20.611224 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_linear.rds
2025-11-22 10:01:20.745004 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_linear.rds
2025-11-22 10:01:20.980272 WARNING::Deleting existing residuals file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/residuals_logistic.rds
2025-11-22 10:01:21.794281 WARNING::Deleting existing fitted file: /tmp/RtmpWKJx9v/file181aa4da499e0/fits/fitted_logistic.rds
2025-11-22 10:02:02.415089 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-22 10:02:02.43461 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-22 10:02:02.463734 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-22 10:02:02.564408 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-22 10:02:02.598916 ERROR::Effect name not found in metadata: d
2025-11-22 10:02:02.618234 ERROR::No user formula provided
2025-11-22 10:02:02.655778 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-22 10:02:02.695161 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-22 10:02:07.627424 INFO::Writing function arguments to log file
2025-11-22 10:02:07.644545 INFO::Verifying options selected are valid
2025-11-22 10:02:11.978189 INFO::Writing function arguments to log file
2025-11-22 10:02:11.992105 INFO::Verifying options selected are valid
2025-11-22 10:02:11.993369 INFO::Determining format of input files
2025-11-22 10:02:11.994382 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-22 10:02:11.996888 INFO::Running selected normalization method: TSS
2025-11-22 10:02:11.998722 INFO::Creating output feature tables folder
2025-11-22 10:02:11.999983 INFO::Writing normalized data to file /tmp/RtmpWKJx9v/file181aab28fa42/features/data_norm.tsv
2025-11-22 10:02:12.001881 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-22 10:02:12.002911 INFO::Total samples in data: 16
2025-11-22 10:02:12.003819 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-22 10:02:12.00466 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-22 10:02:12.00658 INFO::Total filtered features: 0
2025-11-22 10:02:12.007624 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-22 10:02:12.008788 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-22 10:02:12.009719 INFO::Filtered feature names from variance filtering:
2025-11-22 10:02:12.010602 INFO::Writing filtered data to file /tmp/RtmpWKJx9v/file181aab28fa42/features/filtered_data.tsv
2025-11-22 10:02:12.022173 INFO::Running selected transform method: LOG
2025-11-22 10:02:12.023914 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpWKJx9v/file181aab28fa42/features/data_transformed.tsv
2025-11-22 10:02:12.026087 INFO::Applying z-score to standardize continuous metadata
2025-11-22 10:02:12.061543 INFO::Running the linear model component
2025-11-22 10:02:12.090939 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:12.11787 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:12.137371 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:12.1787 INFO::Counting total values for each feature
2025-11-22 10:02:12.181609 INFO::Running the logistic model component
2025-11-22 10:02:12.206659 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:12.214065 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:12.220906 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:12.249228 INFO::Counting total values for each feature
2025-11-22 10:02:12.25237 INFO::Re-running abundances for warn_prevalence
2025-11-22 10:02:12.253576 INFO::Running selected normalization method: TSS
2025-11-22 10:02:12.255347 INFO::Running selected transform method: LOG
2025-11-22 10:02:12.272106 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:12.294848 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:12.299912 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:12.512288 INFO::Creating fits folder
2025-11-22 10:02:12.514101 INFO::Writing residuals to file /tmp/RtmpWKJx9v/file181aab28fa42/fits/residuals_linear.rds
2025-11-22 10:02:12.517777 INFO::Writing fitted values to file /tmp/RtmpWKJx9v/file181aab28fa42/fits/fitted_linear.rds
2025-11-22 10:02:12.520108 INFO::Writing residuals to file /tmp/RtmpWKJx9v/file181aab28fa42/fits/residuals_logistic.rds
2025-11-22 10:02:12.521977 INFO::Writing fitted values to file /tmp/RtmpWKJx9v/file181aab28fa42/fits/fitted_logistic.rds
2025-11-22 10:02:12.54752 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpWKJx9v/file181aab28fa42/all_results.tsv
2025-11-22 10:02:12.558433 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/RtmpWKJx9v/file181aab28fa42/significant_results.tsv
2025-11-22 10:02:12.563362 INFO::Creating output figures folder
2025-11-22 10:02:12.566632 INFO::Writing summary plot of significant
results to file: /tmp/RtmpWKJx9v/file181aab28fa42/figures/summary_plot.pdf
2025-11-22 10:02:16.042696 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpWKJx9v/file181aab28fa42/figures
2025-11-22 10:02:16.045288 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-22 10:02:16.051497 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-22 10:02:17.08092 INFO::Writing summary plot of
significant results to file: /tmp/RtmpWKJx9v/file181aab28fa42/figures/summary_plot.pdf
2025-11-22 10:02:20.587587 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpWKJx9v/file181aab28fa42/figures
2025-11-22 10:02:20.589461 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-22 10:02:20.599904 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-22 10:02:21.895481 INFO::Running the linear model component
2025-11-22 10:02:21.91984 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:21.931214 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:21.940561 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:21.965452 INFO::Counting total values for each feature
2025-11-22 10:02:21.967026 INFO::Running the logistic model component
2025-11-22 10:02:21.981242 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:21.988463 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:21.994395 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:22.003572 INFO::Counting total values for each feature
2025-11-22 10:02:22.0058 INFO::Re-running abundances for warn_prevalence
2025-11-22 10:02:22.006573 INFO::Running selected normalization method: TSS
2025-11-22 10:02:22.007909 INFO::Running selected transform method: LOG
2025-11-22 10:02:22.016187 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:22.020865 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:22.024924 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:22.243493 INFO::Creating output folder
2025-11-22 10:02:22.245153 INFO::Creating output figures folder
2025-11-22 10:02:22.248216 INFO::Writing summary plot of significant
results to file: /tmp/RtmpWKJx9v/file181aa2b7d394b/figures/summary_plot.pdf
2025-11-22 10:02:25.335922 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpWKJx9v/file181aa2b7d394b/figures
2025-11-22 10:02:25.338772 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-22 10:02:25.359106 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-22 10:02:27.413341 INFO::Applying z-score to standardize continuous metadata
2025-11-22 10:02:27.433129 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-22 10:02:27.434188 INFO::Bypass z-score application to metadata
2025-11-22 10:02:27.43672 INFO::Bypass z-score application to metadata
2025-11-22 10:02:27.478691 INFO::Determining format of input files
2025-11-22 10:02:27.480168 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-22 10:02:27.481148 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-22 10:02:27.503323 INFO::Determining format of input files
2025-11-22 10:02:27.504743 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-22 10:02:27.505983 INFO::Input format is feature_specific_covariate samples as columns
2025-11-22 10:02:27.514154 INFO::Determining format of input files
2025-11-22 10:02:27.51523 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-22 10:02:27.516253 INFO::Input format is feature_specific_covariate samples as columns
2025-11-22 10:02:27.51772 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-22 10:02:27.518405 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-22 10:02:27.542257 INFO::Running selected transform method: LOG
2025-11-22 10:02:27.543986 INFO::Creating output feature tables folder
2025-11-22 10:02:27.545201 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpWKJx9v/file181aa351d474d/features/data_transformed.tsv
2025-11-22 10:02:27.553339 INFO::Running selected transform method: LOG
2025-11-22 10:02:27.554633 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpWKJx9v/file181aa351d474d/features/data_transformed.tsv
2025-11-22 10:02:27.558606 INFO::Running selected transform method: PLOG
2025-11-22 10:02:27.560194 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpWKJx9v/file181aa351d474d/features/data_transformed.tsv
2025-11-22 10:02:27.563304 INFO::Running selected transform method: NONE
2025-11-22 10:02:27.564131 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpWKJx9v/file181aa351d474d/features/data_transformed.tsv
2025-11-22 10:02:27.586277 INFO::Running the linear model component
2025-11-22 10:02:27.594868 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:27.599533 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:27.603597 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:27.631885 INFO::Counting total values for each feature
2025-11-22 10:02:27.633869 INFO::Running the logistic model component
2025-11-22 10:02:27.642219 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:27.655594 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:27.661666 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:27.670909 INFO::Counting total values for each feature
2025-11-22 10:02:27.673139 INFO::Re-running abundances for warn_prevalence
2025-11-22 10:02:27.673876 INFO::Running selected normalization method: TSS
2025-11-22 10:02:27.675177 INFO::Running selected transform method: LOG
2025-11-22 10:02:27.703653 INFO::Fitting model to feature number 1, a
2025-11-22 10:02:27.708623 INFO::Fitting model to feature number 2, b
2025-11-22 10:02:27.712723 INFO::Fitting model to feature number 3, c
2025-11-22 10:02:27.897217 INFO::Creating output folder
2025-11-22 10:02:27.898595 INFO::Creating fits folder
2025-11-22 10:02:27.899501 INFO::Writing residuals to file /tmp/RtmpWKJx9v/file181aa15342b79/fits/residuals_linear.rds
2025-11-22 10:02:27.90085 INFO::Writing fitted values to file /tmp/RtmpWKJx9v/file181aa15342b79/fits/fitted_linear.rds
2025-11-22 10:02:27.901928 INFO::Writing residuals to file /tmp/RtmpWKJx9v/file181aa15342b79/fits/residuals_logistic.rds
2025-11-22 10:02:27.903015 INFO::Writing fitted values to file /tmp/RtmpWKJx9v/file181aa15342b79/fits/fitted_logistic.rds
2025-11-22 10:02:27.905829 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpWKJx9v/file181aa15342b79/all_results.tsv
2025-11-22 10:02:27.914074 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/RtmpWKJx9v/file181aa15342b79/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
457.153 9.670 662.371
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 25.845 | 1.092 | 36.788 | |
| maaslin_check_arguments | 0.234 | 0.004 | 0.323 | |
| maaslin_check_formula | 0.203 | 0.010 | 0.260 | |
| maaslin_compute_formula | 0.264 | 0.010 | 0.335 | |
| maaslin_contrast_test | 23.747 | 1.337 | 34.284 | |
| maaslin_filter | 0.727 | 0.056 | 1.171 | |
| maaslin_fit | 16.952 | 1.118 | 24.830 | |
| maaslin_log_arguments | 0.196 | 0.010 | 0.268 | |
| maaslin_normalize | 0.414 | 0.036 | 0.625 | |
| maaslin_plot_results | 54.416 | 1.332 | 77.493 | |
| maaslin_plot_results_from_output | 55.468 | 1.236 | 79.153 | |
| maaslin_process_metadata | 0.742 | 0.058 | 1.196 | |
| maaslin_read_data | 0.187 | 0.008 | 0.226 | |
| maaslin_reorder_data | 0.196 | 0.010 | 0.293 | |
| maaslin_transform | 0.924 | 0.077 | 1.397 | |
| maaslin_write_results | 17.516 | 0.629 | 25.471 | |
| maaslin_write_results_lefse_format | 19.060 | 0.880 | 28.458 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.006 | 0.001 | 0.006 | |