William Nickols
| Snapshot Date: 2026-01-12 13:45 -0500 (Mon, 12 Jan 2026) |
| 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 2026-01-15 11:59 -0500 (Thu, 15 Jan 2026).
| 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" | 4886 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4672 |
| 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 | | ||||||||
| 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: 2026-01-13 10:56:35 -0000 (Tue, 13 Jan 2026) |
| EndedAt: 2026-01-13 11:15:45 -0000 (Tue, 13 Jan 2026) |
| EllapsedTime: 1149.9 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_from_output 72.365 0.386 76.720
maaslin_plot_results 71.048 0.255 75.629
maaslin_contrast_test 33.048 0.310 34.363
maaslin3 32.406 0.357 35.859
maaslin_write_results_lefse_format 27.381 0.076 32.259
maaslin_write_results 26.524 0.262 28.897
maaslin_fit 23.053 0.115 23.514
* 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")
2026-01-13 11:06:31.903506 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:06:32.059908 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:06:32.217532 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:06:32.254956 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:06:32.314284 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:06:32.46631 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:06:32.475331 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:06:32.496105 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:06:32.6662 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:06:32.675284 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:06:32.76726 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:06:32.847655 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:06:32.867459 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:06:32.935664 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:06:33.055112 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:06:58.54553 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:06:58.680465 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:06:58.829779 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:06:58.868834 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:06:58.93097 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:06:59.064311 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:06:59.073264 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:06:59.094897 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:06:59.266809 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:06:59.275204 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:06:59.355647 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:06:59.421969 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:06:59.441271 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:06:59.508594 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:06:59.624546 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:07:35.473702 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:07:35.598952 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:07:35.719543 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:07:35.753922 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:07:35.808323 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:07:35.93425 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:07:35.942844 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:07:35.962935 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:07:36.127402 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:07:36.136017 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:07:36.216319 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:07:36.282803 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:07:36.302218 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:07:36.366761 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:07:36.507309 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:07:57.99305 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:07:58.116432 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:07:58.239892 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:07:58.275285 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:07:58.335014 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:07:58.46568 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:07:58.474775 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:07:58.495363 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:07:58.69429 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:07:58.703161 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:07:58.787318 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:07:58.855948 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:07:58.875696 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:07:58.944437 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:07:59.05851 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:07:59.34478 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/residuals_linear.rds
2026-01-13 11:07:59.41412 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/fitted_linear.rds
2026-01-13 11:07:59.485204 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/residuals_logistic.rds
2026-01-13 11:07:59.835524 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/fitted_logistic.rds
2026-01-13 11:08:32.091963 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:08:32.246794 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:08:32.403199 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:08:32.447272 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:08:32.520116 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:08:32.667966 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:08:32.677531 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:08:32.699233 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:08:32.894697 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:08:32.90348 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:08:32.992455 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:08:33.065511 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:08:33.085927 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:08:33.155489 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:08:33.277453 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:08:54.971031 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:08:55.15317 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:08:55.275868 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:08:55.311746 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:08:55.369697 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:08:55.498172 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:08:55.507987 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:08:55.527444 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:08:55.683399 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:08:55.691935 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:08:55.772844 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:08:55.844441 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:08:55.862958 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:08:55.925698 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:08:56.035617 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:08:56.367476 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/residuals_linear.rds
2026-01-13 11:08:56.435766 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/fitted_linear.rds
2026-01-13 11:08:56.506099 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/residuals_logistic.rds
2026-01-13 11:08:56.849256 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/fitted_logistic.rds
2026-01-13 11:09:26.586826 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:09:26.721368 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:09:26.854604 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:09:26.892534 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:09:26.954319 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:09:27.086683 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:09:27.096014 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:09:27.117051 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:09:27.328721 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:09:27.338248 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:09:27.425267 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:09:27.496272 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:09:27.516488 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:09:27.585242 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:09:27.707794 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:09:49.307365 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:09:49.472877 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:09:49.601714 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:09:49.640312 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:09:49.699171 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:09:49.826493 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:09:49.834982 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:09:49.854487 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:09:50.015104 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:09:50.023876 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:09:50.106684 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:09:50.2071 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:09:50.254653 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:09:50.408454 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:09:50.667718 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:09:50.975371 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/residuals_linear.rds
2026-01-13 11:09:51.044899 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/fitted_linear.rds
2026-01-13 11:09:51.116387 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/residuals_logistic.rds
2026-01-13 11:09:51.464015 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b7d7936f8/fits/fitted_logistic.rds
2026-01-13 11:10:21.382619 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:10:21.51931 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:10:21.657568 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:10:21.694387 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:10:21.754544 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:10:21.892158 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:10:21.901575 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:10:21.922731 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:10:22.092653 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:10:22.102361 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:10:22.191275 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:10:22.26241 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:10:22.283041 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:10:22.35196 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:10:22.472147 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:10:42.899165 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:10:43.055779 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:10:43.218761 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:10:43.256336 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:10:43.316196 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:10:43.455257 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:10:43.463887 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:10:43.484051 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:10:43.651533 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:10:43.66066 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:10:43.748577 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:10:43.822953 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:10:43.845715 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:10:43.920504 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:10:44.081279 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:11:18.523634 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:11:34.08102 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:12:11.001995 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:12:27.38796 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:12:28.40947 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_linear.rds
2026-01-13 11:12:28.504205 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_linear.rds
2026-01-13 11:12:28.596591 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_logistic.rds
2026-01-13 11:12:28.740162 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_logistic.rds
2026-01-13 11:13:01.60137 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:13:12.476214 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:13:13.061575 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_linear.rds
2026-01-13 11:13:13.133841 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_linear.rds
2026-01-13 11:13:13.191585 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_logistic.rds
2026-01-13 11:13:13.270839 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_logistic.rds
2026-01-13 11:13:40.883684 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:13:52.859551 WARNING::Fitting problem for feature 124 returning NA
2026-01-13 11:13:53.427088 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_linear.rds
2026-01-13 11:13:53.568291 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_linear.rds
2026-01-13 11:13:53.661883 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_logistic.rds
2026-01-13 11:13:53.823358 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_logistic.rds
2026-01-13 11:14:20.090189 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:14:20.225943 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:14:20.390935 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:14:20.430618 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:14:20.492381 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:14:20.628789 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:14:20.638494 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:14:20.659411 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:14:20.881658 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:14:20.89125 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:14:20.980245 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:14:21.050052 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:14:21.080058 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:14:21.150918 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:14:21.272594 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:14:43.099063 WARNING::Fitting problem for feature 50 returning NA
2026-01-13 11:14:43.240137 WARNING::Fitting problem for feature 62 returning NA
2026-01-13 11:14:43.382169 WARNING::Fitting problem for feature 74 returning NA
2026-01-13 11:14:43.425307 WARNING::Fitting problem for feature 78 returning NA
2026-01-13 11:14:43.487491 WARNING::Fitting problem for feature 84 returning NA
2026-01-13 11:14:43.621772 WARNING::Fitting problem for feature 96 returning NA
2026-01-13 11:14:43.631063 WARNING::Fitting problem for feature 97 returning NA
2026-01-13 11:14:43.651842 WARNING::Fitting problem for feature 99 returning NA
2026-01-13 11:14:43.824565 WARNING::Fitting problem for feature 114 returning NA
2026-01-13 11:14:43.833717 WARNING::Fitting problem for feature 115 returning NA
2026-01-13 11:14:43.920874 WARNING::Fitting problem for feature 123 returning NA
2026-01-13 11:14:43.994176 WARNING::Fitting problem for feature 130 returning NA
2026-01-13 11:14:44.035657 WARNING::Fitting problem for feature 132 returning NA
2026-01-13 11:14:44.185907 WARNING::Fitting problem for feature 139 returning NA
2026-01-13 11:14:44.329502 WARNING::Fitting problem for feature 150 returning NA
2026-01-13 11:14:44.75928 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_linear.rds
2026-01-13 11:14:44.828711 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_linear.rds
2026-01-13 11:14:44.900196 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/residuals_logistic.rds
2026-01-13 11:14:45.256896 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3fa8cb40/fits/fitted_logistic.rds
2026-01-13 11:15:16.981931 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-01-13 11:15:17.008449 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-01-13 11:15:17.027632 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-01-13 11:15:17.113039 ERROR::No fixed, group, or
ordered effects included in formula.
2026-01-13 11:15:17.140977 ERROR::Effect name not found in metadata: d
2026-01-13 11:15:17.172286 ERROR::No user formula provided
2026-01-13 11:15:17.268456 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-01-13 11:15:17.30711 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-01-13 11:15:22.395479 INFO::Writing function arguments to log file
2026-01-13 11:15:22.417112 INFO::Verifying options selected are valid
2026-01-13 11:15:25.851644 INFO::Writing function arguments to log file
2026-01-13 11:15:25.876574 INFO::Verifying options selected are valid
2026-01-13 11:15:25.878247 INFO::Determining format of input files
2026-01-13 11:15:25.87975 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-13 11:15:25.883463 INFO::Running selected normalization method: TSS
2026-01-13 11:15:25.885854 INFO::Creating output feature tables folder
2026-01-13 11:15:25.887563 INFO::Writing normalized data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/features/data_norm.tsv
2026-01-13 11:15:25.890016 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-01-13 11:15:25.8917 INFO::Total samples in data: 16
2026-01-13 11:15:25.89313 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-01-13 11:15:25.894564 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-01-13 11:15:25.897727 INFO::Total filtered features: 0
2026-01-13 11:15:25.899432 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-01-13 11:15:25.901333 INFO::Total features filtered by non-zero variance filtering: 0
2026-01-13 11:15:25.902897 INFO::Filtered feature names from variance filtering:
2026-01-13 11:15:25.904246 INFO::Writing filtered data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/features/filtered_data.tsv
2026-01-13 11:15:25.906623 INFO::Running selected transform method: LOG
2026-01-13 11:15:25.908635 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/features/data_transformed.tsv
2026-01-13 11:15:25.9113 INFO::Applying z-score to standardize continuous metadata
2026-01-13 11:15:25.919862 INFO::Running the linear model component
2026-01-13 11:15:25.942785 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:25.950191 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:25.957235 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:25.96934 INFO::Counting total values for each feature
2026-01-13 11:15:25.972782 INFO::Running the logistic model component
2026-01-13 11:15:25.99635 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:26.007342 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:26.01807 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:26.033097 INFO::Counting total values for each feature
2026-01-13 11:15:26.036858 INFO::Re-running abundances for warn_prevalence
2026-01-13 11:15:26.038578 INFO::Running selected normalization method: TSS
2026-01-13 11:15:26.041172 INFO::Running selected transform method: LOG
2026-01-13 11:15:26.064882 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:26.072385 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:26.079912 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:26.232434 INFO::Creating fits folder
2026-01-13 11:15:26.234656 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/fits/residuals_linear.rds
2026-01-13 11:15:26.236793 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/fits/fitted_linear.rds
2026-01-13 11:15:26.239424 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/fits/residuals_logistic.rds
2026-01-13 11:15:26.241661 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/fits/fitted_logistic.rds
2026-01-13 11:15:26.246354 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/all_results.tsv
2026-01-13 11:15:26.249295 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/Rtmp3dURh0/file3d670b2f32a33f/significant_results.tsv
2026-01-13 11:15:26.251878 INFO::Creating output figures folder
2026-01-13 11:15:26.25443 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/figures/summary_plot.pdf
2026-01-13 11:15:28.721534 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/figures
2026-01-13 11:15:28.72479 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-13 11:15:28.733111 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-13 11:15:29.50139 INFO::Writing summary plot of
significant results to file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/figures/summary_plot.pdf
2026-01-13 11:15:32.143746 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b2f32a33f/figures
2026-01-13 11:15:32.146182 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-13 11:15:32.154241 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-13 11:15:32.897244 INFO::Running the linear model component
2026-01-13 11:15:32.912045 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:32.91929 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:32.925866 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:32.937154 INFO::Counting total values for each feature
2026-01-13 11:15:32.939935 INFO::Running the logistic model component
2026-01-13 11:15:32.954045 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:32.964489 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:32.974495 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:32.988548 INFO::Counting total values for each feature
2026-01-13 11:15:32.991884 INFO::Re-running abundances for warn_prevalence
2026-01-13 11:15:32.993212 INFO::Running selected normalization method: TSS
2026-01-13 11:15:32.995479 INFO::Running selected transform method: LOG
2026-01-13 11:15:33.01027 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:33.017569 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:33.024823 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:33.165727 INFO::Creating output folder
2026-01-13 11:15:33.16727 INFO::Creating output figures folder
2026-01-13 11:15:33.169326 INFO::Writing summary plot of significant
results to file: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3dfb7c58/figures/summary_plot.pdf
2026-01-13 11:15:35.513126 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/Rtmp3dURh0/file3d670b3dfb7c58/figures
2026-01-13 11:15:35.515852 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-13 11:15:35.523613 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-13 11:15:37.021635 INFO::Applying z-score to standardize continuous metadata
2026-01-13 11:15:37.033877 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-01-13 11:15:37.035243 INFO::Bypass z-score application to metadata
2026-01-13 11:15:37.03892 INFO::Bypass z-score application to metadata
2026-01-13 11:15:37.065428 INFO::Determining format of input files
2026-01-13 11:15:37.066883 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-13 11:15:37.068119 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-01-13 11:15:37.079156 INFO::Determining format of input files
2026-01-13 11:15:37.081018 INFO::Input format is data samples as columns and metadata samples as rows
2026-01-13 11:15:37.083154 INFO::Input format is feature_specific_covariate samples as columns
2026-01-13 11:15:37.095952 INFO::Determining format of input files
2026-01-13 11:15:37.097658 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-13 11:15:37.099336 INFO::Input format is feature_specific_covariate samples as columns
2026-01-13 11:15:37.101999 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-01-13 11:15:37.103434 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-01-13 11:15:37.121 INFO::Running selected transform method: LOG
2026-01-13 11:15:37.122827 INFO::Creating output feature tables folder
2026-01-13 11:15:37.124167 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b24268d64/features/data_transformed.tsv
2026-01-13 11:15:37.130646 INFO::Running selected transform method: LOG
2026-01-13 11:15:37.132436 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b24268d64/features/data_transformed.tsv
2026-01-13 11:15:37.138614 INFO::Running selected transform method: PLOG
2026-01-13 11:15:37.141351 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b24268d64/features/data_transformed.tsv
2026-01-13 11:15:37.146317 INFO::Running selected transform method: NONE
2026-01-13 11:15:37.147688 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b24268d64/features/data_transformed.tsv
2026-01-13 11:15:37.159322 INFO::Running the linear model component
2026-01-13 11:15:37.174908 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:37.182268 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:37.189007 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:37.199634 INFO::Counting total values for each feature
2026-01-13 11:15:37.202358 INFO::Running the logistic model component
2026-01-13 11:15:37.217109 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:37.227501 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:37.237037 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:37.251199 INFO::Counting total values for each feature
2026-01-13 11:15:37.254619 INFO::Re-running abundances for warn_prevalence
2026-01-13 11:15:37.255857 INFO::Running selected normalization method: TSS
2026-01-13 11:15:37.258038 INFO::Running selected transform method: LOG
2026-01-13 11:15:37.27296 INFO::Fitting model to feature number 1, a
2026-01-13 11:15:37.279768 INFO::Fitting model to feature number 2, b
2026-01-13 11:15:37.286378 INFO::Fitting model to feature number 3, c
2026-01-13 11:15:37.426265 INFO::Creating output folder
2026-01-13 11:15:37.43312 INFO::Creating fits folder
2026-01-13 11:15:37.434718 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b583014c0/fits/residuals_linear.rds
2026-01-13 11:15:37.436172 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b583014c0/fits/fitted_linear.rds
2026-01-13 11:15:37.437822 INFO::Writing residuals to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b583014c0/fits/residuals_logistic.rds
2026-01-13 11:15:37.439325 INFO::Writing fitted values to file /home/biocbuild/tmp/Rtmp3dURh0/file3d670b583014c0/fits/fitted_logistic.rds
2026-01-13 11:15:37.447452 INFO::Writing all the results to file (ordered
by increasing individual q-values): /home/biocbuild/tmp/Rtmp3dURh0/file3d670b583014c0/all_results.tsv
2026-01-13 11:15:37.454218 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/Rtmp3dURh0/file3d670b583014c0/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
520.413 5.582 562.939
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 32.406 | 0.357 | 35.859 | |
| maaslin_check_arguments | 0.272 | 0.000 | 0.541 | |
| maaslin_check_formula | 0.274 | 0.016 | 0.583 | |
| maaslin_compute_formula | 0.324 | 0.008 | 0.366 | |
| maaslin_contrast_test | 33.048 | 0.310 | 34.363 | |
| maaslin_filter | 0.754 | 0.004 | 0.771 | |
| maaslin_fit | 23.053 | 0.115 | 23.514 | |
| maaslin_log_arguments | 0.237 | 0.008 | 0.245 | |
| maaslin_normalize | 0.434 | 0.000 | 0.434 | |
| maaslin_plot_results | 71.048 | 0.255 | 75.629 | |
| maaslin_plot_results_from_output | 72.365 | 0.386 | 76.720 | |
| maaslin_process_metadata | 0.738 | 0.027 | 0.769 | |
| maaslin_read_data | 0.247 | 0.008 | 0.275 | |
| maaslin_reorder_data | 0.270 | 0.000 | 0.271 | |
| maaslin_transform | 0.930 | 0.020 | 0.952 | |
| maaslin_write_results | 26.524 | 0.262 | 28.897 | |
| maaslin_write_results_lefse_format | 27.381 | 0.076 | 32.259 | |
| preprocess_dna_mtx | 0.006 | 0.000 | 0.006 | |
| preprocess_taxa_mtx | 0.007 | 0.000 | 0.007 | |