William Nickols
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 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 2025-12-22 12:07 -0500 (Mon, 22 Dec 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" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: maaslin3 |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-12-19 11:10:10 -0000 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 11:27:30 -0000 (Fri, 19 Dec 2025) |
| EllapsedTime: 1039.5 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_1.2.0.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 ‘1.2.0’
* 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 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 64.308 0.466 64.955
maaslin_plot_results_from_output 63.795 0.458 64.416
maaslin_contrast_test 29.489 1.025 30.629
maaslin3 28.789 0.376 29.247
maaslin_write_results_lefse_format 23.974 0.044 24.073
maaslin_write_results 23.030 0.251 23.334
maaslin_fit 20.960 0.404 21.448
* 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 ‘1.2.0’ ** 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 4.5.0 (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")
2025-12-19 11:18:49.962488 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:18:50.099574 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:18:50.248266 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:18:50.283757 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:18:50.338449 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:18:50.4717 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:18:50.480162 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:18:50.499122 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:18:50.652734 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:18:50.661251 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:18:50.742125 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:18:50.819448 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:18:50.839305 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:18:50.908847 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:18:51.028216 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:19:13.631026 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:19:13.757215 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:19:13.90067 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:19:13.936694 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:19:13.991698 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:19:14.113834 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:19:14.12219 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:19:14.140905 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:19:14.294504 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:19:14.302974 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:19:14.386687 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:19:14.452471 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:19:14.471941 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:19:14.541896 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:19:14.659949 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:19:46.686002 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:19:46.816247 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:19:46.940349 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:19:46.976552 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:19:47.034641 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:19:47.164316 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:19:47.17306 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:19:47.192785 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:19:47.347709 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:19:47.356378 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:19:47.436613 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:19:47.504968 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:19:47.524706 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:19:47.593491 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:19:47.718788 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:20:07.845914 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:20:07.966432 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:20:08.08395 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:20:08.120011 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:20:08.1747 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:20:08.297565 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:20:08.305864 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:20:08.324385 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:20:08.503965 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:20:08.512353 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:20:08.591455 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:20:08.655063 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:20:08.674082 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:20:08.741587 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:20:08.851576 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:20:09.133315 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/residuals_linear.rds
2025-12-19 11:20:09.194002 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/fitted_linear.rds
2025-12-19 11:20:09.256673 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/residuals_logistic.rds
2025-12-19 11:20:09.549726 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/fitted_logistic.rds
2025-12-19 11:20:41.22039 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:20:41.391835 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:20:41.557891 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:20:41.60671 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:20:41.685517 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:20:41.857292 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:20:41.868647 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:20:41.894892 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:20:42.138259 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:20:42.149304 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:20:42.247509 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:20:42.328982 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:20:42.353044 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:20:42.435948 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:20:42.577745 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:21:03.936435 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:21:04.067186 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:21:04.199348 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:21:04.241334 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:21:04.309587 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:21:04.460189 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:21:04.470171 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:21:04.493878 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:21:04.684143 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:21:04.694732 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:21:04.795326 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:21:04.881082 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:21:04.904093 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:21:04.984495 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:21:05.125305 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:21:05.483934 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/residuals_linear.rds
2025-12-19 11:21:05.553258 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/fitted_linear.rds
2025-12-19 11:21:05.62461 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/residuals_logistic.rds
2025-12-19 11:21:05.972091 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/fitted_logistic.rds
2025-12-19 11:21:36.608452 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:21:36.751017 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:21:36.90325 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:21:36.948408 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:21:37.019665 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:21:37.179195 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:21:37.190088 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:21:37.214615 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:21:37.455778 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:21:37.466543 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:21:37.568532 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:21:37.650534 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:21:37.674061 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:21:37.756027 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:21:37.900681 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:21:59.347722 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:21:59.526804 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:21:59.664489 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:21:59.704947 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:21:59.767204 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:21:59.906204 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:21:59.915417 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:21:59.9359 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:22:00.110628 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:22:00.119924 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:22:00.213761 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:22:00.296501 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:22:00.320268 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:22:00.405471 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:22:00.551323 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:22:00.877581 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/residuals_linear.rds
2025-12-19 11:22:00.947039 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/fitted_linear.rds
2025-12-19 11:22:01.018355 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/residuals_logistic.rds
2025-12-19 11:22:01.368868 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e527e48a09/fits/fitted_logistic.rds
2025-12-19 11:22:31.454598 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:22:31.591197 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:22:31.720357 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:22:31.75749 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:22:31.819335 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:22:31.949054 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:22:31.957841 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:22:31.977796 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:22:32.148597 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:22:32.158074 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:22:32.248264 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:22:32.320631 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:22:32.342957 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:22:32.413163 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:22:32.53226 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:22:51.764979 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:22:51.89056 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:22:52.014488 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:22:52.05046 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:22:52.108661 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:22:52.235874 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:22:52.244276 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:22:52.263811 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:22:52.429763 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:22:52.439465 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:22:52.531842 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:22:52.604123 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:22:52.62449 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:22:52.693538 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:22:52.85001 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:23:26.053001 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:23:41.377445 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:24:15.433897 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:24:29.737602 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:24:30.694525 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_linear.rds
2025-12-19 11:24:30.763151 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_linear.rds
2025-12-19 11:24:30.805944 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_logistic.rds
2025-12-19 11:24:30.882988 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_logistic.rds
2025-12-19 11:25:01.925245 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:25:11.212177 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:25:11.701554 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_linear.rds
2025-12-19 11:25:11.764378 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_linear.rds
2025-12-19 11:25:11.805561 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_logistic.rds
2025-12-19 11:25:11.880452 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_logistic.rds
2025-12-19 11:25:37.312989 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:25:46.950133 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 11:25:47.503591 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_linear.rds
2025-12-19 11:25:47.573386 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_linear.rds
2025-12-19 11:25:47.617335 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_logistic.rds
2025-12-19 11:25:47.695147 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_logistic.rds
2025-12-19 11:26:12.699632 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:26:12.842762 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:26:13.022934 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:26:13.064611 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:26:13.129618 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:26:13.272911 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:26:13.282941 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:26:13.303855 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:26:13.473803 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:26:13.483375 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:26:13.574065 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:26:13.646595 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:26:13.667354 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:26:13.739701 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:26:13.861633 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:26:34.26076 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 11:26:34.382438 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 11:26:34.50378 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 11:26:34.53969 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 11:26:34.598388 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 11:26:34.726509 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 11:26:34.73509 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 11:26:34.754918 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 11:26:34.925015 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 11:26:34.934096 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 11:26:35.065066 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 11:26:35.135092 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 11:26:35.15541 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 11:26:35.229818 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 11:26:35.360376 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 11:26:35.747999 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_linear.rds
2025-12-19 11:26:35.817007 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_linear.rds
2025-12-19 11:26:35.888102 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/residuals_logistic.rds
2025-12-19 11:26:36.231662 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e5392b0bbc/fits/fitted_logistic.rds
2025-12-19 11:27:04.945605 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-19 11:27:04.973772 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-19 11:27:04.992985 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-19 11:27:05.079225 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-19 11:27:05.106491 ERROR::Effect name not found in metadata: d
2025-12-19 11:27:05.12519 ERROR::No user formula provided
2025-12-19 11:27:05.175067 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-19 11:27:05.194437 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-19 11:27:10.342492 INFO::Writing function arguments to log file
2025-12-19 11:27:10.367984 INFO::Verifying options selected are valid
2025-12-19 11:27:13.916301 INFO::Writing function arguments to log file
2025-12-19 11:27:13.936948 INFO::Verifying options selected are valid
2025-12-19 11:27:13.938542 INFO::Determining format of input files
2025-12-19 11:27:13.940003 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-19 11:27:13.943671 INFO::Running selected normalization method: TSS
2025-12-19 11:27:13.946189 INFO::Creating output feature tables folder
2025-12-19 11:27:13.947929 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/features/data_norm.tsv
2025-12-19 11:27:13.950406 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-19 11:27:13.951939 INFO::Total samples in data: 16
2025-12-19 11:27:13.95355 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-19 11:27:13.954982 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-19 11:27:13.958263 INFO::Total filtered features: 0
2025-12-19 11:27:13.96 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-19 11:27:13.961915 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-19 11:27:13.963449 INFO::Filtered feature names from variance filtering:
2025-12-19 11:27:13.964929 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/features/filtered_data.tsv
2025-12-19 11:27:13.967201 INFO::Running selected transform method: LOG
2025-12-19 11:27:13.969109 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/features/data_transformed.tsv
2025-12-19 11:27:13.971685 INFO::Applying z-score to standardize continuous metadata
2025-12-19 11:27:13.979353 INFO::Running the linear model component
2025-12-19 11:27:14.00268 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:14.010344 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:14.017622 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:14.029084 INFO::Counting total values for each feature
2025-12-19 11:27:14.03196 INFO::Running the logistic model component
2025-12-19 11:27:14.056114 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:14.066275 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:14.076784 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:14.091888 INFO::Counting total values for each feature
2025-12-19 11:27:14.095396 INFO::Re-running abundances for warn_prevalence
2025-12-19 11:27:14.097107 INFO::Running selected normalization method: TSS
2025-12-19 11:27:14.099566 INFO::Running selected transform method: LOG
2025-12-19 11:27:14.123069 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:14.130109 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:14.137327 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:14.276129 INFO::Creating fits folder
2025-12-19 11:27:14.277973 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/fits/residuals_linear.rds
2025-12-19 11:27:14.279643 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/fits/fitted_linear.rds
2025-12-19 11:27:14.281468 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/fits/residuals_logistic.rds
2025-12-19 11:27:14.283283 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/fits/fitted_logistic.rds
2025-12-19 11:27:14.287471 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/all_results.tsv
2025-12-19 11:27:14.29031 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/Rtmp6GYt9l/file1766e52e1ee673/significant_results.tsv
2025-12-19 11:27:14.292479 INFO::Creating output figures folder
2025-12-19 11:27:14.294709 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/figures/summary_plot.pdf
2025-12-19 11:27:16.671537 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/figures
2025-12-19 11:27:16.674637 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-19 11:27:16.682411 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-19 11:27:17.467215 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/figures/summary_plot.pdf
2025-12-19 11:27:19.845646 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e52e1ee673/figures
2025-12-19 11:27:19.847963 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-19 11:27:19.85579 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-19 11:27:20.621122 INFO::Running the linear model component
2025-12-19 11:27:20.638488 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:20.647271 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:20.65627 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:20.669719 INFO::Counting total values for each feature
2025-12-19 11:27:20.67268 INFO::Running the logistic model component
2025-12-19 11:27:20.6901 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:20.702429 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:20.714092 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:20.730746 INFO::Counting total values for each feature
2025-12-19 11:27:20.7347 INFO::Re-running abundances for warn_prevalence
2025-12-19 11:27:20.73642 INFO::Running selected normalization method: TSS
2025-12-19 11:27:20.739145 INFO::Running selected transform method: LOG
2025-12-19 11:27:20.756104 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:20.763127 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:20.770533 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:20.939862 INFO::Creating output folder
2025-12-19 11:27:20.941421 INFO::Creating output figures folder
2025-12-19 11:27:20.943449 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e53ae4a534/figures/summary_plot.pdf
2025-12-19 11:27:23.330287 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp6GYt9l/file1766e53ae4a534/figures
2025-12-19 11:27:23.333 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-19 11:27:23.340983 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-19 11:27:24.813093 INFO::Applying z-score to standardize continuous metadata
2025-12-19 11:27:24.825288 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-19 11:27:24.826709 INFO::Bypass z-score application to metadata
2025-12-19 11:27:24.830751 INFO::Bypass z-score application to metadata
2025-12-19 11:27:24.85879 INFO::Determining format of input files
2025-12-19 11:27:24.860267 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-19 11:27:24.861609 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-19 11:27:24.873127 INFO::Determining format of input files
2025-12-19 11:27:24.874891 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-19 11:27:24.87708 INFO::Input format is feature_specific_covariate samples as columns
2025-12-19 11:27:24.89011 INFO::Determining format of input files
2025-12-19 11:27:24.891713 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-19 11:27:24.893516 INFO::Input format is feature_specific_covariate samples as columns
2025-12-19 11:27:24.896148 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-19 11:27:24.897603 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-19 11:27:24.913763 INFO::Running selected transform method: LOG
2025-12-19 11:27:24.915461 INFO::Creating output feature tables folder
2025-12-19 11:27:24.916929 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e57548b0fc/features/data_transformed.tsv
2025-12-19 11:27:24.923454 INFO::Running selected transform method: LOG
2025-12-19 11:27:24.925411 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e57548b0fc/features/data_transformed.tsv
2025-12-19 11:27:24.931579 INFO::Running selected transform method: PLOG
2025-12-19 11:27:24.93438 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e57548b0fc/features/data_transformed.tsv
2025-12-19 11:27:24.938975 INFO::Running selected transform method: NONE
2025-12-19 11:27:24.940503 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e57548b0fc/features/data_transformed.tsv
2025-12-19 11:27:24.951541 INFO::Running the linear model component
2025-12-19 11:27:24.966691 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:24.973968 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:24.981242 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:24.992315 INFO::Counting total values for each feature
2025-12-19 11:27:24.994953 INFO::Running the logistic model component
2025-12-19 11:27:25.009719 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:25.019397 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:25.028716 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:25.043236 INFO::Counting total values for each feature
2025-12-19 11:27:25.04651 INFO::Re-running abundances for warn_prevalence
2025-12-19 11:27:25.047875 INFO::Running selected normalization method: TSS
2025-12-19 11:27:25.050176 INFO::Running selected transform method: LOG
2025-12-19 11:27:25.06465 INFO::Fitting model to feature number 1, a
2025-12-19 11:27:25.071476 INFO::Fitting model to feature number 2, b
2025-12-19 11:27:25.07943 INFO::Fitting model to feature number 3, c
2025-12-19 11:27:25.21926 INFO::Creating output folder
2025-12-19 11:27:25.220904 INFO::Creating fits folder
2025-12-19 11:27:25.222401 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e568b1d7f/fits/residuals_linear.rds
2025-12-19 11:27:25.224088 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e568b1d7f/fits/fitted_linear.rds
2025-12-19 11:27:25.225945 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e568b1d7f/fits/residuals_logistic.rds
2025-12-19 11:27:25.227768 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp6GYt9l/file1766e568b1d7f/fits/fitted_logistic.rds
2025-12-19 11:27:25.231809 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp6GYt9l/file1766e568b1d7f/all_results.tsv
2025-12-19 11:27:25.234605 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/Rtmp6GYt9l/file1766e568b1d7f/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
523.253 4.900 529.444
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 28.789 | 0.376 | 29.247 | |
| maaslin_check_arguments | 0.203 | 0.003 | 0.208 | |
| maaslin_check_formula | 0.205 | 0.003 | 0.207 | |
| maaslin_compute_formula | 0.251 | 0.001 | 0.252 | |
| maaslin_contrast_test | 29.489 | 1.025 | 30.629 | |
| maaslin_filter | 0.651 | 0.008 | 0.662 | |
| maaslin_fit | 20.960 | 0.404 | 21.448 | |
| maaslin_log_arguments | 0.195 | 0.009 | 0.204 | |
| maaslin_normalize | 0.372 | 0.012 | 0.385 | |
| maaslin_plot_results | 64.308 | 0.466 | 64.955 | |
| maaslin_plot_results_from_output | 63.795 | 0.458 | 64.416 | |
| maaslin_process_metadata | 0.655 | 0.024 | 0.680 | |
| maaslin_read_data | 0.203 | 0.000 | 0.204 | |
| maaslin_reorder_data | 0.214 | 0.000 | 0.215 | |
| maaslin_transform | 0.822 | 0.012 | 0.835 | |
| maaslin_write_results | 23.030 | 0.251 | 23.334 | |
| maaslin_write_results_lefse_format | 23.974 | 0.044 | 24.073 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.001 | 0.004 | 0.006 | |