William Nickols
| Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: e7106d5 |
| git_last_commit_date: 2025-10-12 11:00:51 -0400 (Sun, 12 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-20 12:07 -0400 (Mon, 20 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 1164/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.2 (landing page) William Nickols
| nebbiolo2 | 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 | | ||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.1.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.2.tar.gz |
| StartedAt: 2025-10-17 10:37:28 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 10:54:47 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 1039.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.2’
* 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 loading without being on the library search path ... 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 64.501 0.684 65.416
maaslin_plot_results_from_output 63.515 0.535 64.251
maaslin_contrast_test 29.243 1.110 30.488
maaslin3 28.940 0.418 29.445
maaslin_write_results_lefse_format 24.925 0.168 25.168
maaslin_write_results 22.106 0.148 22.329
maaslin_fit 21.197 0.604 21.900
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.1.2’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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")
2025-10-17 10:46:05.713757 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:46:05.859029 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:46:06.028891 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:46:06.067061 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:46:06.125232 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:46:06.248387 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:46:06.25685 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:46:06.276039 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:46:06.44668 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:46:06.455384 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:46:06.537556 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:46:06.602365 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:46:06.621417 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:46:06.699759 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:46:06.815782 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:46:31.780494 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:46:31.925282 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:46:32.084673 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:46:32.121724 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:46:32.182109 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:46:32.318927 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:46:32.328128 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:46:32.349419 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:46:32.522192 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:46:32.531499 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:46:32.621535 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:46:32.694489 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:46:32.715979 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:46:32.793329 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:46:32.907979 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:47:06.116331 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:47:06.24262 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:47:06.364724 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:47:06.399001 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:47:06.45418 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:47:06.579158 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:47:06.587518 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:47:06.606163 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:47:06.763989 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:47:06.772767 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:47:06.856531 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:47:06.928521 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:47:06.948659 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:47:07.013762 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:47:07.127209 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:47:27.532435 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:47:27.688831 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:47:27.819573 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:47:27.856209 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:47:27.913527 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:47:28.036244 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:47:28.044526 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:47:28.063475 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:47:28.217795 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:47:28.226242 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:47:28.30524 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:47:28.370013 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:47:28.38934 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:47:28.454577 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:47:28.565553 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:47:28.851686 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/residuals_linear.rds
2025-10-17 10:47:28.919727 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/fitted_linear.rds
2025-10-17 10:47:28.990056 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/residuals_logistic.rds
2025-10-17 10:47:29.331125 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/fitted_logistic.rds
2025-10-17 10:47:58.58287 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:47:58.714088 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:47:58.843358 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:47:58.882384 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:47:58.942997 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:47:59.083085 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:47:59.092406 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:47:59.112916 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:47:59.272884 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:47:59.282259 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:47:59.370198 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:47:59.441917 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:47:59.464137 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:47:59.53668 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:48:00.665424 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:48:21.199728 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:48:21.328886 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:48:21.456251 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:48:21.494034 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:48:21.551641 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:48:21.678831 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:48:21.687003 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:48:21.705558 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:48:21.853268 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:48:21.861381 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:48:21.93712 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:48:22.000541 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:48:22.022206 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:48:22.097698 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:48:22.224508 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:48:22.574339 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/residuals_linear.rds
2025-10-17 10:48:22.638051 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/fitted_linear.rds
2025-10-17 10:48:22.703214 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/residuals_logistic.rds
2025-10-17 10:48:23.018795 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/fitted_logistic.rds
2025-10-17 10:48:52.823929 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:48:52.962288 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:48:53.091871 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:48:53.127123 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:48:53.188313 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:48:53.322429 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:48:53.331486 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:48:53.351977 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:48:53.527843 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:48:53.537097 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:48:53.626476 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:48:53.698421 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:48:53.719136 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:48:53.791414 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:48:53.919826 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:49:12.326538 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:49:12.454775 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:49:12.577609 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:49:12.612671 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:49:12.670038 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:49:12.793431 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:49:12.801732 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:49:12.820565 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:49:12.978998 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:49:12.988639 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:49:13.119266 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:49:13.190234 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:49:13.210431 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:49:13.280664 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:49:13.40219 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:49:13.704912 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/residuals_linear.rds
2025-10-17 10:49:13.773978 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/fitted_linear.rds
2025-10-17 10:49:13.845088 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/residuals_logistic.rds
2025-10-17 10:49:14.19009 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a2f2422ad/fits/fitted_logistic.rds
2025-10-17 10:49:42.884662 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:49:43.018805 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:49:43.151076 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:49:43.189789 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:49:43.248254 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:49:43.380461 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:49:43.389589 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:49:43.411088 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:49:43.583703 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:49:43.592594 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:49:43.71615 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:49:43.78773 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:49:43.808822 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:49:43.881599 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:49:44.002234 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:50:04.185198 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:50:04.333448 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:50:04.46976 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:50:04.507875 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:50:04.567654 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:50:04.702099 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:50:04.711059 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:50:04.731743 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:50:04.908519 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:50:04.918545 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:50:05.010017 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:50:05.08205 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:50:05.103802 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:50:05.178077 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:50:05.304934 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:50:38.658776 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:50:55.316443 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:51:30.85033 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:51:45.037998 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:51:46.108407 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_linear.rds
2025-10-17 10:51:46.180339 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_linear.rds
2025-10-17 10:51:46.22553 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_logistic.rds
2025-10-17 10:51:46.307371 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_logistic.rds
2025-10-17 10:52:18.308212 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:52:27.813959 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:52:28.292763 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_linear.rds
2025-10-17 10:52:28.360834 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_linear.rds
2025-10-17 10:52:28.405017 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_logistic.rds
2025-10-17 10:52:28.494389 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_logistic.rds
2025-10-17 10:52:54.541854 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:53:04.176791 WARNING::Fitting problem for feature 124 returning NA
2025-10-17 10:53:04.661726 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_linear.rds
2025-10-17 10:53:04.724036 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_linear.rds
2025-10-17 10:53:04.765859 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_logistic.rds
2025-10-17 10:53:04.842244 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_logistic.rds
2025-10-17 10:53:30.066589 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:53:30.245101 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:53:30.378253 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:53:30.41871 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:53:30.483416 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:53:30.617703 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:53:30.626925 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:53:30.64812 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:53:30.816346 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:53:30.825562 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:53:30.910496 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:53:30.977277 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:53:30.997215 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:53:31.066334 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:53:31.183541 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:53:51.167741 WARNING::Fitting problem for feature 50 returning NA
2025-10-17 10:53:51.295499 WARNING::Fitting problem for feature 62 returning NA
2025-10-17 10:53:51.420888 WARNING::Fitting problem for feature 74 returning NA
2025-10-17 10:53:51.457675 WARNING::Fitting problem for feature 78 returning NA
2025-10-17 10:53:51.557957 WARNING::Fitting problem for feature 84 returning NA
2025-10-17 10:53:51.691165 WARNING::Fitting problem for feature 96 returning NA
2025-10-17 10:53:51.700216 WARNING::Fitting problem for feature 97 returning NA
2025-10-17 10:53:51.720265 WARNING::Fitting problem for feature 99 returning NA
2025-10-17 10:53:51.885114 WARNING::Fitting problem for feature 114 returning NA
2025-10-17 10:53:51.893741 WARNING::Fitting problem for feature 115 returning NA
2025-10-17 10:53:51.986736 WARNING::Fitting problem for feature 123 returning NA
2025-10-17 10:53:52.054163 WARNING::Fitting problem for feature 130 returning NA
2025-10-17 10:53:52.074548 WARNING::Fitting problem for feature 132 returning NA
2025-10-17 10:53:52.141306 WARNING::Fitting problem for feature 139 returning NA
2025-10-17 10:53:52.257378 WARNING::Fitting problem for feature 150 returning NA
2025-10-17 10:53:52.625567 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_linear.rds
2025-10-17 10:53:52.695274 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_linear.rds
2025-10-17 10:53:52.767192 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/residuals_logistic.rds
2025-10-17 10:53:53.115246 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a63028cc5/fits/fitted_logistic.rds
2025-10-17 10:54:21.511724 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-10-17 10:54:21.544816 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-10-17 10:54:21.564221 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-10-17 10:54:21.650785 ERROR::No fixed, group, or
ordered effects included in formula.
2025-10-17 10:54:21.677847 ERROR::Effect name not found in metadata: d
2025-10-17 10:54:21.696215 ERROR::No user formula provided
2025-10-17 10:54:21.744153 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-10-17 10:54:21.763732 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-10-17 10:54:27.222524 INFO::Writing function arguments to log file
2025-10-17 10:54:27.247407 INFO::Verifying options selected are valid
2025-10-17 10:54:30.844139 INFO::Writing function arguments to log file
2025-10-17 10:54:30.865106 INFO::Verifying options selected are valid
2025-10-17 10:54:30.866798 INFO::Determining format of input files
2025-10-17 10:54:30.868286 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-17 10:54:30.872177 INFO::Running selected normalization method: TSS
2025-10-17 10:54:30.874931 INFO::Creating output feature tables folder
2025-10-17 10:54:30.876982 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/features/data_norm.tsv
2025-10-17 10:54:30.879833 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-10-17 10:54:30.881743 INFO::Total samples in data: 16
2025-10-17 10:54:30.88346 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-10-17 10:54:30.885075 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-10-17 10:54:30.888355 INFO::Total filtered features: 0
2025-10-17 10:54:30.890137 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-10-17 10:54:30.892219 INFO::Total features filtered by non-zero variance filtering: 0
2025-10-17 10:54:30.893976 INFO::Filtered feature names from variance filtering:
2025-10-17 10:54:30.89556 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/features/filtered_data.tsv
2025-10-17 10:54:30.898295 INFO::Running selected transform method: LOG
2025-10-17 10:54:30.900445 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/features/data_transformed.tsv
2025-10-17 10:54:30.903426 INFO::Applying z-score to standardize continuous metadata
2025-10-17 10:54:30.911915 INFO::Running the linear model component
2025-10-17 10:54:30.936112 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:30.943974 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:30.952221 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:30.964778 INFO::Counting total values for each feature
2025-10-17 10:54:30.968033 INFO::Running the logistic model component
2025-10-17 10:54:30.992954 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:31.003726 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:31.014943 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:31.02998 INFO::Counting total values for each feature
2025-10-17 10:54:31.033556 INFO::Re-running abundances for warn_prevalence
2025-10-17 10:54:31.035201 INFO::Running selected normalization method: TSS
2025-10-17 10:54:31.037805 INFO::Running selected transform method: LOG
2025-10-17 10:54:31.060681 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:31.067493 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:31.0745 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:31.214526 INFO::Creating fits folder
2025-10-17 10:54:31.216261 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/fits/residuals_linear.rds
2025-10-17 10:54:31.218016 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/fits/fitted_linear.rds
2025-10-17 10:54:31.219838 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/fits/residuals_logistic.rds
2025-10-17 10:54:31.221807 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/fits/fitted_logistic.rds
2025-10-17 10:54:31.226177 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/all_results.tsv
2025-10-17 10:54:31.228844 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): /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/significant_results.tsv
2025-10-17 10:54:31.2309 INFO::Creating output figures folder
2025-10-17 10:54:31.233006 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/figures/summary_plot.pdf
2025-10-17 10:54:33.689776 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/figures
2025-10-17 10:54:33.693048 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-17 10:54:33.701807 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-17 10:54:34.494267 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/figures/summary_plot.pdf
2025-10-17 10:54:36.86151 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a4bceeb74/figures
2025-10-17 10:54:36.864135 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-17 10:54:36.872703 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-17 10:54:37.642264 INFO::Running the linear model component
2025-10-17 10:54:37.657105 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:37.663903 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:37.670264 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:37.681311 INFO::Counting total values for each feature
2025-10-17 10:54:37.683963 INFO::Running the logistic model component
2025-10-17 10:54:37.697898 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:37.707539 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:37.716941 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:37.730309 INFO::Counting total values for each feature
2025-10-17 10:54:37.733503 INFO::Re-running abundances for warn_prevalence
2025-10-17 10:54:37.734811 INFO::Running selected normalization method: TSS
2025-10-17 10:54:37.736976 INFO::Running selected transform method: LOG
2025-10-17 10:54:37.751342 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:37.757935 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:37.764121 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:37.901265 INFO::Creating output folder
2025-10-17 10:54:37.90274 INFO::Creating output figures folder
2025-10-17 10:54:37.904612 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a51b850dd/figures/summary_plot.pdf
2025-10-17 10:54:40.286671 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a51b850dd/figures
2025-10-17 10:54:40.289563 INFO::Plotting associations from most to least significant, grouped by metadata
2025-10-17 10:54:40.297704 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-10-17 10:54:41.764577 INFO::Applying z-score to standardize continuous metadata
2025-10-17 10:54:41.777067 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-10-17 10:54:41.778409 INFO::Bypass z-score application to metadata
2025-10-17 10:54:41.782308 INFO::Bypass z-score application to metadata
2025-10-17 10:54:41.810445 INFO::Determining format of input files
2025-10-17 10:54:41.811938 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-17 10:54:41.813404 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-10-17 10:54:41.82516 INFO::Determining format of input files
2025-10-17 10:54:41.826889 INFO::Input format is data samples as columns and metadata samples as rows
2025-10-17 10:54:41.829023 INFO::Input format is feature_specific_covariate samples as columns
2025-10-17 10:54:41.842371 INFO::Determining format of input files
2025-10-17 10:54:41.844009 INFO::Input format is data samples as rows and metadata samples as rows
2025-10-17 10:54:41.845741 INFO::Input format is feature_specific_covariate samples as columns
2025-10-17 10:54:41.848555 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-10-17 10:54:41.849986 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-10-17 10:54:41.867328 INFO::Running selected transform method: LOG
2025-10-17 10:54:41.869159 INFO::Creating output feature tables folder
2025-10-17 10:54:41.870615 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1bd380ff/features/data_transformed.tsv
2025-10-17 10:54:41.876867 INFO::Running selected transform method: LOG
2025-10-17 10:54:41.87876 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1bd380ff/features/data_transformed.tsv
2025-10-17 10:54:41.884957 INFO::Running selected transform method: PLOG
2025-10-17 10:54:41.887776 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1bd380ff/features/data_transformed.tsv
2025-10-17 10:54:41.892434 INFO::Running selected transform method: NONE
2025-10-17 10:54:41.893883 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1bd380ff/features/data_transformed.tsv
2025-10-17 10:54:41.933121 INFO::Running the linear model component
2025-10-17 10:54:41.948116 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:41.95498 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:41.961572 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:41.972822 INFO::Counting total values for each feature
2025-10-17 10:54:41.975583 INFO::Running the logistic model component
2025-10-17 10:54:41.989414 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:41.999188 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:42.008576 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:42.022435 INFO::Counting total values for each feature
2025-10-17 10:54:42.025691 INFO::Re-running abundances for warn_prevalence
2025-10-17 10:54:42.02704 INFO::Running selected normalization method: TSS
2025-10-17 10:54:42.02921 INFO::Running selected transform method: LOG
2025-10-17 10:54:42.043018 INFO::Fitting model to feature number 1, a
2025-10-17 10:54:42.049433 INFO::Fitting model to feature number 2, b
2025-10-17 10:54:42.055927 INFO::Fitting model to feature number 3, c
2025-10-17 10:54:42.195499 INFO::Creating output folder
2025-10-17 10:54:42.197042 INFO::Creating fits folder
2025-10-17 10:54:42.198355 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1ec7ac88/fits/residuals_linear.rds
2025-10-17 10:54:42.199797 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1ec7ac88/fits/fitted_linear.rds
2025-10-17 10:54:42.201334 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1ec7ac88/fits/residuals_logistic.rds
2025-10-17 10:54:42.202838 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1ec7ac88/fits/fitted_logistic.rds
2025-10-17 10:54:42.206702 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1ec7ac88/all_results.tsv
2025-10-17 10:54:42.209098 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): /home/biocbuild/tmp/Rtmp7VAETS/file2bc38a1ec7ac88/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
520.213 9.358 531.160
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.940 | 0.418 | 29.445 | |
| maaslin_check_arguments | 0.204 | 0.004 | 0.208 | |
| maaslin_check_formula | 0.209 | 0.000 | 0.209 | |
| maaslin_compute_formula | 0.241 | 0.004 | 0.245 | |
| maaslin_contrast_test | 29.243 | 1.110 | 30.488 | |
| maaslin_filter | 0.640 | 0.028 | 0.671 | |
| maaslin_fit | 21.197 | 0.604 | 21.900 | |
| maaslin_log_arguments | 0.197 | 0.000 | 0.198 | |
| maaslin_normalize | 0.361 | 0.012 | 0.375 | |
| maaslin_plot_results | 64.501 | 0.684 | 65.416 | |
| maaslin_plot_results_from_output | 63.515 | 0.535 | 64.251 | |
| maaslin_process_metadata | 0.643 | 0.031 | 0.677 | |
| maaslin_read_data | 0.195 | 0.000 | 0.196 | |
| maaslin_reorder_data | 0.200 | 0.004 | 0.205 | |
| maaslin_transform | 0.745 | 0.030 | 0.778 | |
| maaslin_write_results | 22.106 | 0.148 | 22.329 | |
| maaslin_write_results_lefse_format | 24.925 | 0.168 | 25.168 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.002 | 0.004 | 0.006 | |