William Nickols
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: d4f80f8 |
| git_last_commit_date: 2026-02-09 12:23:40 -0400 (Mon, 09 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1190/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| See other builds for maaslin3 in R Universe. | ||||||||||||||
|
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: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2026-04-17 04:36:14 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 04:51:30 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 915.8 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 67.766 0.251 68.190
maaslin_plot_results_from_output 67.147 0.251 67.562
maaslin_contrast_test 31.060 0.351 31.478
maaslin3 29.106 0.798 29.995
maaslin_write_results_lefse_format 26.359 0.067 26.487
maaslin_write_results 23.924 0.164 24.152
maaslin_fit 22.449 0.092 22.589
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck/00check.log’
for details.
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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")
2026-04-17 04:42:12.45 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:42:12.61 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:42:12.76 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:42:12.79 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:42:12.86 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:42:13.00 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:42:13.01 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:42:13.03 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:42:13.20 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:42:13.21 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:42:13.30 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:42:13.38 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:42:13.40 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:42:13.47 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:42:13.60 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:42:36.64 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:42:36.76 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:42:36.90 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:42:36.95 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:42:37.01 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:42:37.14 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:42:37.15 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:42:37.17 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:42:37.34 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:42:37.35 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:42:37.43 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:42:37.51 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:42:37.53 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:42:37.60 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:42:37.72 WARNING::Fitting problem for feature 150 returning NA
Warning: stack imbalance in '::', 52 then 54
Warning: stack imbalance in '<-', 50 then 52
2026-04-17 04:43:18.98 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:43:19.11 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:43:19.25 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:43:19.29 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:43:19.36 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:43:19.50 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:43:19.51 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:43:19.53 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:43:19.72 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:43:19.73 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:43:19.82 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:43:19.90 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:43:19.92 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:43:20.00 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:43:20.13 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:43:41.18 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:43:41.31 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:43:41.44 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:43:41.48 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:43:41.54 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:43:42.78 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:43:42.79 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:43:42.82 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:43:42.99 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:43:42.99 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:43:43.08 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:43:43.15 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:43:43.17 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:43:43.25 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:43:43.37 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:43:43.69 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/residuals_linear.rds
2026-04-17 04:43:43.76 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/fitted_linear.rds
2026-04-17 04:43:43.84 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/residuals_logistic.rds
2026-04-17 04:43:44.19 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/fitted_logistic.rds
2026-04-17 04:44:16.32 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:44:16.46 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:44:16.59 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:44:16.63 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:44:16.69 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:44:16.82 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:44:16.83 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:44:16.85 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:44:17.02 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:44:17.03 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:44:17.11 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:44:17.18 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:44:17.20 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:44:17.28 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:44:17.40 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:44:39.20 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:44:39.33 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:44:39.46 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:44:39.50 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:44:39.56 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:44:39.69 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:44:39.70 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:44:39.72 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:44:39.89 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:44:39.90 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:44:39.98 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:44:40.05 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:44:40.07 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:44:40.14 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:44:40.25 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:44:40.54 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/residuals_linear.rds
2026-04-17 04:44:40.60 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/fitted_linear.rds
2026-04-17 04:44:40.66 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/residuals_logistic.rds
2026-04-17 04:44:41.01 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/fitted_logistic.rds
2026-04-17 04:45:12.07 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:45:12.21 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:45:12.35 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:45:12.39 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:45:12.45 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:45:12.59 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:45:12.60 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:45:12.62 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:45:12.80 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:45:12.81 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:45:12.90 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:45:12.97 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:45:12.99 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:45:13.07 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:45:13.20 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:45:35.57 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:45:35.71 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:45:35.85 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:45:35.89 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:45:35.95 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:45:36.10 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:45:36.11 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:45:36.13 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:45:36.31 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:45:36.32 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:45:36.42 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:45:36.49 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:45:36.51 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:45:36.59 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:45:36.71 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:45:37.09 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/residuals_linear.rds
2026-04-17 04:45:37.15 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/fitted_linear.rds
2026-04-17 04:45:37.22 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/residuals_logistic.rds
2026-04-17 04:45:37.54 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb497547a0f6/fits/fitted_logistic.rds
2026-04-17 04:46:08.19 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:46:08.34 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:46:08.49 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:46:08.53 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:46:08.60 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:46:08.74 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:46:08.75 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:46:08.77 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:46:08.99 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:46:09.00 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:46:09.09 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:46:09.17 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:46:09.19 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:46:09.27 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:46:09.40 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:46:31.66 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:46:31.80 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:46:31.93 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:46:31.98 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:46:32.04 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:46:32.18 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:46:32.19 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:46:32.21 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:46:32.38 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:46:32.39 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:46:32.48 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:46:32.55 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:46:32.57 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:46:32.64 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:46:32.76 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:47:07.48 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:47:25.21 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:48:01.68 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:48:17.63 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:48:20.25 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_linear.rds
2026-04-17 04:48:20.32 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_linear.rds
2026-04-17 04:48:20.36 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_logistic.rds
2026-04-17 04:48:20.45 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_logistic.rds
2026-04-17 04:48:53.24 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:49:02.46 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:49:03.05 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_linear.rds
2026-04-17 04:49:03.12 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_linear.rds
2026-04-17 04:49:03.16 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_logistic.rds
2026-04-17 04:49:03.24 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_logistic.rds
2026-04-17 04:49:32.25 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:49:41.53 WARNING::Fitting problem for feature 124 returning NA
2026-04-17 04:49:42.06 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_linear.rds
2026-04-17 04:49:42.12 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_linear.rds
2026-04-17 04:49:42.17 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_logistic.rds
2026-04-17 04:49:42.25 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_logistic.rds
2026-04-17 04:50:09.26 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:50:09.40 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:50:09.54 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:50:09.58 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:50:09.65 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:50:09.79 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:50:09.80 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:50:09.82 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:50:10.04 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:50:10.06 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:50:10.16 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:50:10.24 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:50:10.26 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:50:10.34 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:50:10.47 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:50:33.07 WARNING::Fitting problem for feature 50 returning NA
2026-04-17 04:50:33.21 WARNING::Fitting problem for feature 62 returning NA
2026-04-17 04:50:33.35 WARNING::Fitting problem for feature 74 returning NA
2026-04-17 04:50:33.39 WARNING::Fitting problem for feature 78 returning NA
2026-04-17 04:50:33.45 WARNING::Fitting problem for feature 84 returning NA
2026-04-17 04:50:33.60 WARNING::Fitting problem for feature 96 returning NA
2026-04-17 04:50:33.61 WARNING::Fitting problem for feature 97 returning NA
2026-04-17 04:50:33.63 WARNING::Fitting problem for feature 99 returning NA
2026-04-17 04:50:33.80 WARNING::Fitting problem for feature 114 returning NA
2026-04-17 04:50:33.81 WARNING::Fitting problem for feature 115 returning NA
2026-04-17 04:50:33.91 WARNING::Fitting problem for feature 123 returning NA
2026-04-17 04:50:33.98 WARNING::Fitting problem for feature 130 returning NA
2026-04-17 04:50:34.00 WARNING::Fitting problem for feature 132 returning NA
2026-04-17 04:50:34.09 WARNING::Fitting problem for feature 139 returning NA
2026-04-17 04:50:34.21 WARNING::Fitting problem for feature 150 returning NA
2026-04-17 04:50:34.66 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_linear.rds
2026-04-17 04:50:34.73 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_linear.rds
2026-04-17 04:50:34.81 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/residuals_logistic.rds
2026-04-17 04:50:35.16 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49393ae6c0/fits/fitted_logistic.rds
2026-04-17 04:51:04.74 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-04-17 04:51:04.77 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-04-17 04:51:04.79 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-04-17 04:51:04.87 ERROR::No fixed, group, or
ordered effects included in formula.
2026-04-17 04:51:04.90 ERROR::Effect name not found in metadata: d
2026-04-17 04:51:04.93 ERROR::No user formula provided
2026-04-17 04:51:04.98 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-04-17 04:51:05.00 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-04-17 04:51:10.16 INFO::Writing function arguments to log file
2026-04-17 04:51:10.20 INFO::Verifying options selected are valid
2026-04-17 04:51:13.81 INFO::Writing function arguments to log file
2026-04-17 04:51:13.84 INFO::Verifying options selected are valid
2026-04-17 04:51:13.84 INFO::Determining format of input files
2026-04-17 04:51:13.84 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-17 04:51:13.85 INFO::Running selected normalization method: TSS
2026-04-17 04:51:13.85 INFO::Creating output feature tables folder
2026-04-17 04:51:13.85 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/features/data_norm.tsv
2026-04-17 04:51:13.85 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-04-17 04:51:13.86 INFO::Total samples in data: 16
2026-04-17 04:51:13.86 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-04-17 04:51:13.86 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-04-17 04:51:13.86 INFO::Total filtered features: 0
2026-04-17 04:51:13.87 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-04-17 04:51:13.87 INFO::Total features filtered by non-zero variance filtering: 0
2026-04-17 04:51:13.87 INFO::Filtered feature names from variance filtering:
2026-04-17 04:51:13.87 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/features/filtered_data.tsv
2026-04-17 04:51:13.87 INFO::Running selected transform method: LOG
2026-04-17 04:51:13.88 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/features/data_transformed.tsv
2026-04-17 04:51:13.88 INFO::Applying z-score to standardize continuous metadata
2026-04-17 04:51:13.89 INFO::Running the linear model component
2026-04-17 04:51:13.92 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:13.93 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:13.93 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:13.95 INFO::Counting total values for each feature
2026-04-17 04:51:13.95 INFO::Running the logistic model component
2026-04-17 04:51:13.98 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:13.99 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:14.00 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:14.02 INFO::Counting total values for each feature
2026-04-17 04:51:14.02 INFO::Re-running abundances for warn_prevalence
2026-04-17 04:51:14.02 INFO::Running selected normalization method: TSS
2026-04-17 04:51:14.02 INFO::Running selected transform method: LOG
2026-04-17 04:51:14.05 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:14.06 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:14.07 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:14.22 INFO::Creating fits folder
2026-04-17 04:51:14.22 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/fits/residuals_linear.rds
2026-04-17 04:51:14.22 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/fits/fitted_linear.rds
2026-04-17 04:51:14.23 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/fits/residuals_logistic.rds
2026-04-17 04:51:14.23 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/fits/fitted_logistic.rds
2026-04-17 04:51:14.23 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/all_results.tsv
2026-04-17 04:51:14.24 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/RtmpRIhdDx/file1deb49ad254f4/significant_results.tsv
2026-04-17 04:51:14.24 INFO::Creating output figures folder
2026-04-17 04:51:14.24 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/figures/summary_plot.pdf
2026-04-17 04:51:16.72 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/figures
2026-04-17 04:51:16.73 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-17 04:51:16.73 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-17 04:51:17.51 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/figures/summary_plot.pdf
2026-04-17 04:51:19.97 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRIhdDx/file1deb49ad254f4/figures
2026-04-17 04:51:19.98 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-17 04:51:19.98 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-17 04:51:20.79 INFO::Running the linear model component
2026-04-17 04:51:20.80 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:20.81 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:20.82 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:20.83 INFO::Counting total values for each feature
2026-04-17 04:51:20.83 INFO::Running the logistic model component
2026-04-17 04:51:20.85 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:20.86 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:20.87 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:20.88 INFO::Counting total values for each feature
2026-04-17 04:51:20.88 INFO::Re-running abundances for warn_prevalence
2026-04-17 04:51:20.89 INFO::Running selected normalization method: TSS
2026-04-17 04:51:20.89 INFO::Running selected transform method: LOG
2026-04-17 04:51:20.90 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:20.91 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:20.92 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:21.07 INFO::Creating output folder
2026-04-17 04:51:21.07 INFO::Creating output figures folder
2026-04-17 04:51:21.07 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/RtmpRIhdDx/file1deb4927ac639/figures/summary_plot.pdf
2026-04-17 04:51:23.52 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpRIhdDx/file1deb4927ac639/figures
2026-04-17 04:51:23.52 INFO::Plotting associations from most to least significant, grouped by metadata
2026-04-17 04:51:23.53 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-04-17 04:51:25.08 INFO::Applying z-score to standardize continuous metadata
2026-04-17 04:51:25.10 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-04-17 04:51:25.10 INFO::Bypass z-score application to metadata
2026-04-17 04:51:25.10 INFO::Bypass z-score application to metadata
2026-04-17 04:51:25.17 INFO::Determining format of input files
2026-04-17 04:51:25.17 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-17 04:51:25.18 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-04-17 04:51:25.19 INFO::Determining format of input files
2026-04-17 04:51:25.19 INFO::Input format is data samples as columns and metadata samples as rows
2026-04-17 04:51:25.19 INFO::Input format is feature_specific_covariate samples as columns
2026-04-17 04:51:25.21 INFO::Determining format of input files
2026-04-17 04:51:25.21 INFO::Input format is data samples as rows and metadata samples as rows
2026-04-17 04:51:25.21 INFO::Input format is feature_specific_covariate samples as columns
2026-04-17 04:51:25.21 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-04-17 04:51:25.22 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-04-17 04:51:25.23 INFO::Running selected transform method: LOG
2026-04-17 04:51:25.23 INFO::Creating output feature tables folder
2026-04-17 04:51:25.24 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb4927048a30/features/data_transformed.tsv
2026-04-17 04:51:25.24 INFO::Running selected transform method: LOG
2026-04-17 04:51:25.24 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb4927048a30/features/data_transformed.tsv
2026-04-17 04:51:25.25 INFO::Running selected transform method: PLOG
2026-04-17 04:51:25.25 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb4927048a30/features/data_transformed.tsv
2026-04-17 04:51:25.26 INFO::Running selected transform method: NONE
2026-04-17 04:51:25.26 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb4927048a30/features/data_transformed.tsv
2026-04-17 04:51:25.27 INFO::Running the linear model component
2026-04-17 04:51:25.29 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:25.29 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:25.30 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:25.31 INFO::Counting total values for each feature
2026-04-17 04:51:25.32 INFO::Running the logistic model component
2026-04-17 04:51:25.33 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:25.34 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:25.35 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:25.36 INFO::Counting total values for each feature
2026-04-17 04:51:25.37 INFO::Re-running abundances for warn_prevalence
2026-04-17 04:51:25.37 INFO::Running selected normalization method: TSS
2026-04-17 04:51:25.37 INFO::Running selected transform method: LOG
2026-04-17 04:51:25.39 INFO::Fitting model to feature number 1, a
2026-04-17 04:51:25.39 INFO::Fitting model to feature number 2, b
2026-04-17 04:51:25.42 INFO::Fitting model to feature number 3, c
2026-04-17 04:51:25.57 INFO::Creating output folder
2026-04-17 04:51:25.57 INFO::Creating fits folder
2026-04-17 04:51:25.57 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb493c7a6181/fits/residuals_linear.rds
2026-04-17 04:51:25.57 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb493c7a6181/fits/fitted_linear.rds
2026-04-17 04:51:25.57 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb493c7a6181/fits/residuals_logistic.rds
2026-04-17 04:51:25.58 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpRIhdDx/file1deb493c7a6181/fits/fitted_logistic.rds
2026-04-17 04:51:25.58 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/RtmpRIhdDx/file1deb493c7a6181/all_results.tsv
2026-04-17 04:51:25.58 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/RtmpRIhdDx/file1deb493c7a6181/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 96 ]
>
>
> proc.time()
user system elapsed
550.912 5.301 557.579
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 29.106 | 0.798 | 29.995 | |
| maaslin_check_arguments | 0.190 | 0.004 | 0.195 | |
| maaslin_check_formula | 0.230 | 0.000 | 0.231 | |
| maaslin_compute_formula | 0.255 | 0.000 | 0.256 | |
| maaslin_contrast_test | 31.060 | 0.351 | 31.478 | |
| maaslin_filter | 0.686 | 0.012 | 0.700 | |
| maaslin_fit | 22.449 | 0.092 | 22.589 | |
| maaslin_log_arguments | 0.232 | 0.000 | 0.233 | |
| maaslin_normalize | 0.403 | 0.012 | 0.416 | |
| maaslin_plot_results | 67.766 | 0.251 | 68.190 | |
| maaslin_plot_results_from_output | 67.147 | 0.251 | 67.562 | |
| maaslin_process_metadata | 0.699 | 0.020 | 0.721 | |
| maaslin_read_data | 0.210 | 0.004 | 0.214 | |
| maaslin_reorder_data | 0.227 | 0.000 | 0.227 | |
| maaslin_transform | 0.859 | 0.015 | 0.875 | |
| maaslin_write_results | 23.924 | 0.164 | 24.152 | |
| maaslin_write_results_lefse_format | 26.359 | 0.067 | 26.487 | |
| preprocess_dna_mtx | 0.005 | 0.001 | 0.005 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.006 | |