William Nickols
| Snapshot Date: 2026-01-01 13:40 -0500 (Thu, 01 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-03 11:34 -0500 (Sat, 03 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4809 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1158/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2026-01-02 00:47:35 -0500 (Fri, 02 Jan 2026) |
| EndedAt: 2026-01-02 01:09:28 -0500 (Fri, 02 Jan 2026) |
| EllapsedTime: 1312.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 ... 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 43.979 0.452 44.435
maaslin_plot_results 43.064 0.370 43.412
maaslin3 19.529 0.732 20.264
maaslin_contrast_test 18.563 0.553 19.116
maaslin_write_results_lefse_format 15.569 0.083 15.652
maaslin_write_results 13.030 0.143 13.175
maaslin_fit 12.378 0.186 12.564
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/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) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
2026-01-02 00:53:54.974695 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:53:55.052714 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:53:55.14796 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:53:55.174627 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:53:55.221666 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:53:55.299493 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:53:55.304948 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:53:55.317279 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:53:55.426412 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:53:55.431802 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:53:55.481634 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:53:55.522166 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:53:55.534154 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:53:55.574781 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:53:55.655591 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:54:12.238763 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:54:12.317431 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:54:12.408257 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:54:12.432996 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:54:12.472364 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:54:12.579209 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:54:12.585622 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:54:12.599459 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:54:12.704837 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:54:12.710497 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:54:12.762711 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:54:12.805112 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:54:12.817664 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:54:12.859381 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:54:12.930554 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:54:37.356542 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:54:37.440219 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:54:37.519722 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:54:37.542349 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:54:37.577753 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:54:37.657119 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:54:37.663006 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:54:37.675545 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:54:37.774112 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:54:37.779968 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:54:37.834296 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:54:37.878382 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:54:37.89106 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:54:37.933286 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:54:38.007057 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:54:51.199777 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:54:51.278933 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:54:51.355907 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:54:51.378431 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:54:51.414057 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:54:51.497612 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:54:51.503337 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:54:51.515976 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:54:51.618729 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:54:51.624341 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:54:51.676216 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:54:51.717572 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:54:51.729779 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:54:51.771743 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:54:51.864821 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:54:52.066963 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/residuals_linear.rds
2026-01-02 00:54:52.128961 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/fitted_linear.rds
2026-01-02 00:54:52.192929 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/residuals_logistic.rds
2026-01-02 00:54:52.496203 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/fitted_logistic.rds
2026-01-02 00:55:14.263022 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:55:14.355639 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:55:14.434832 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:55:14.45764 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:55:14.493628 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:55:14.573763 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:55:14.579411 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:55:14.591815 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:55:14.701561 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:55:14.708507 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:55:14.769768 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:55:14.817544 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:55:14.830949 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:55:14.877596 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:55:14.957365 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:55:28.000812 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:55:28.079268 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:55:28.155315 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:55:28.177585 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:55:28.213134 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:55:28.29044 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:55:28.296022 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:55:28.307937 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:55:28.408241 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:55:28.414396 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:55:28.505315 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:55:28.549152 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:55:28.56211 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:55:28.617871 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:55:28.692594 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:55:28.919423 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/residuals_linear.rds
2026-01-02 00:55:28.981613 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/fitted_linear.rds
2026-01-02 00:55:29.04607 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/residuals_logistic.rds
2026-01-02 00:55:29.351195 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/fitted_logistic.rds
2026-01-02 00:55:51.796449 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:55:51.874525 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:55:51.952837 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:55:51.976084 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:55:52.011094 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:55:52.087478 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:55:52.092815 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:55:52.10469 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:55:52.202336 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:55:52.208336 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:55:52.261029 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:55:52.30425 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:55:52.317012 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:55:52.359292 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:55:52.431314 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:56:03.328609 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:56:03.4069 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:56:03.482811 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:56:03.505088 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:56:03.539893 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:56:03.618067 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:56:03.623866 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:56:03.635978 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:56:03.733879 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:56:03.739629 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:56:03.793551 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:56:03.836107 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:56:03.84874 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:56:03.892268 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:56:03.966915 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:56:04.231838 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/residuals_linear.rds
2026-01-02 00:56:04.2941 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/fitted_linear.rds
2026-01-02 00:56:04.35838 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/residuals_logistic.rds
2026-01-02 00:56:04.662905 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca1473339af/fits/fitted_logistic.rds
2026-01-02 00:56:26.007036 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:56:26.087521 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:56:26.16568 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:56:26.188831 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:56:26.225029 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:56:26.304669 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:56:26.31023 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:56:26.322672 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:56:26.453607 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:56:26.459858 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:56:26.51414 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:56:26.556665 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:56:26.569203 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:56:26.610974 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:56:26.682784 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:56:38.910269 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:56:38.987651 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:56:39.067842 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:56:39.130161 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:56:39.167414 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:56:39.248576 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:56:39.254115 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:56:39.266272 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:56:39.366444 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:56:39.372157 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:56:39.423279 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:56:39.465245 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:56:39.477878 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:56:39.52033 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:56:39.593616 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:57:03.571068 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:57:13.063304 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:57:40.343658 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:57:49.502248 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:57:50.200473 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_linear.rds
2026-01-02 00:57:50.263933 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_linear.rds
2026-01-02 00:57:50.304395 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_logistic.rds
2026-01-02 00:57:50.377093 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_logistic.rds
2026-01-02 00:58:12.854463 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:58:18.479218 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:58:18.79487 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_linear.rds
2026-01-02 00:58:18.857687 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_linear.rds
2026-01-02 00:58:18.89742 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_logistic.rds
2026-01-02 00:58:18.970247 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_logistic.rds
2026-01-02 00:58:37.99306 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:58:44.537049 WARNING::Fitting problem for feature 124 returning NA
2026-01-02 00:58:44.922986 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_linear.rds
2026-01-02 00:58:44.986226 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_linear.rds
2026-01-02 00:58:45.026311 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_logistic.rds
2026-01-02 00:58:45.10113 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_logistic.rds
2026-01-02 00:59:03.315909 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:59:03.400946 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:59:03.484622 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:59:03.50963 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:59:03.549907 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:59:03.635498 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:59:03.641357 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:59:03.654723 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:59:03.7875 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:59:03.793617 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:59:03.848148 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:59:03.892843 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:59:03.905806 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:59:03.948213 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:59:04.021488 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:59:16.27451 WARNING::Fitting problem for feature 50 returning NA
2026-01-02 00:59:16.355195 WARNING::Fitting problem for feature 62 returning NA
2026-01-02 00:59:16.436228 WARNING::Fitting problem for feature 74 returning NA
2026-01-02 00:59:16.461284 WARNING::Fitting problem for feature 78 returning NA
2026-01-02 00:59:16.498753 WARNING::Fitting problem for feature 84 returning NA
2026-01-02 00:59:16.577129 WARNING::Fitting problem for feature 96 returning NA
2026-01-02 00:59:16.582693 WARNING::Fitting problem for feature 97 returning NA
2026-01-02 00:59:16.595782 WARNING::Fitting problem for feature 99 returning NA
2026-01-02 00:59:16.692455 WARNING::Fitting problem for feature 114 returning NA
2026-01-02 00:59:16.698063 WARNING::Fitting problem for feature 115 returning NA
2026-01-02 00:59:16.74905 WARNING::Fitting problem for feature 123 returning NA
2026-01-02 00:59:16.791471 WARNING::Fitting problem for feature 130 returning NA
2026-01-02 00:59:16.803889 WARNING::Fitting problem for feature 132 returning NA
2026-01-02 00:59:16.845255 WARNING::Fitting problem for feature 139 returning NA
2026-01-02 00:59:16.917364 WARNING::Fitting problem for feature 150 returning NA
2026-01-02 00:59:17.220478 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_linear.rds
2026-01-02 00:59:17.282795 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_linear.rds
2026-01-02 00:59:17.347128 WARNING::Deleting existing residuals file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/residuals_logistic.rds
2026-01-02 00:59:17.651462 WARNING::Deleting existing fitted file: /tmp/Rtmp9Qceg7/file2d9ca163034bdc/fits/fitted_logistic.rds
2026-01-02 00:59:37.88549 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-01-02 00:59:37.902963 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-01-02 00:59:37.914717 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-01-02 00:59:37.967748 ERROR::No fixed, group, or
ordered effects included in formula.
2026-01-02 00:59:37.985165 ERROR::Effect name not found in metadata: d
2026-01-02 00:59:37.997049 ERROR::No user formula provided
2026-01-02 00:59:38.028767 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-01-02 00:59:38.040771 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-01-02 00:59:40.988782 INFO::Writing function arguments to log file
2026-01-02 00:59:41.004014 INFO::Verifying options selected are valid
2026-01-02 00:59:43.446206 INFO::Writing function arguments to log file
2026-01-02 00:59:43.458888 INFO::Verifying options selected are valid
2026-01-02 00:59:43.46006 INFO::Determining format of input files
2026-01-02 00:59:43.461116 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-02 00:59:43.463674 INFO::Running selected normalization method: TSS
2026-01-02 00:59:43.465217 INFO::Creating output feature tables folder
2026-01-02 00:59:43.466232 INFO::Writing normalized data to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/features/data_norm.tsv
2026-01-02 00:59:43.467758 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-01-02 00:59:43.468686 INFO::Total samples in data: 16
2026-01-02 00:59:43.469593 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-01-02 00:59:43.470526 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-01-02 00:59:43.472526 INFO::Total filtered features: 0
2026-01-02 00:59:43.473501 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-01-02 00:59:43.474725 INFO::Total features filtered by non-zero variance filtering: 0
2026-01-02 00:59:43.475734 INFO::Filtered feature names from variance filtering:
2026-01-02 00:59:43.47664 INFO::Writing filtered data to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/features/filtered_data.tsv
2026-01-02 00:59:43.47816 INFO::Running selected transform method: LOG
2026-01-02 00:59:43.479405 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/features/data_transformed.tsv
2026-01-02 00:59:43.481159 INFO::Applying z-score to standardize continuous metadata
2026-01-02 00:59:43.486828 INFO::Running the linear model component
2026-01-02 00:59:43.500998 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:43.505874 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:43.510471 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:43.518132 INFO::Counting total values for each feature
2026-01-02 00:59:43.520074 INFO::Running the logistic model component
2026-01-02 00:59:43.53433 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:43.541426 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:43.54792 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:43.557269 INFO::Counting total values for each feature
2026-01-02 00:59:43.559499 INFO::Re-running abundances for warn_prevalence
2026-01-02 00:59:43.560457 INFO::Running selected normalization method: TSS
2026-01-02 00:59:43.561974 INFO::Running selected transform method: LOG
2026-01-02 00:59:43.576008 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:43.580721 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:43.585126 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:43.675171 INFO::Creating fits folder
2026-01-02 00:59:43.676507 INFO::Writing residuals to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/fits/residuals_linear.rds
2026-01-02 00:59:43.677738 INFO::Writing fitted values to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/fits/fitted_linear.rds
2026-01-02 00:59:43.679031 INFO::Writing residuals to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/fits/residuals_logistic.rds
2026-01-02 00:59:43.680286 INFO::Writing fitted values to file /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/fits/fitted_logistic.rds
2026-01-02 00:59:43.683082 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/all_results.tsv
2026-01-02 00:59:43.684805 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/significant_results.tsv
2026-01-02 00:59:43.686218 INFO::Creating output figures folder
2026-01-02 00:59:43.68767 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/figures/summary_plot.pdf
2026-01-02 00:59:45.26977 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/figures
2026-01-02 00:59:45.271824 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-02 00:59:45.276998 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-02 00:59:45.833268 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/figures/summary_plot.pdf
2026-01-02 00:59:47.50209 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9Qceg7/file2d9ca1efdc7fd/figures
2026-01-02 00:59:47.503901 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-02 00:59:47.509284 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-02 00:59:48.041544 INFO::Running the linear model component
2026-01-02 00:59:48.051328 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:48.056006 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:48.060176 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:48.06742 INFO::Counting total values for each feature
2026-01-02 00:59:48.069117 INFO::Running the logistic model component
2026-01-02 00:59:48.077602 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:48.08374 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:48.089548 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:48.098443 INFO::Counting total values for each feature
2026-01-02 00:59:48.10055 INFO::Re-running abundances for warn_prevalence
2026-01-02 00:59:48.101394 INFO::Running selected normalization method: TSS
2026-01-02 00:59:48.102826 INFO::Running selected transform method: LOG
2026-01-02 00:59:48.111869 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:48.116632 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:48.120856 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:48.21365 INFO::Creating output folder
2026-01-02 00:59:48.214708 INFO::Creating output figures folder
2026-01-02 00:59:48.216097 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp9Qceg7/file2d9ca13fa1fc4e/figures/summary_plot.pdf
2026-01-02 00:59:49.825443 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp9Qceg7/file2d9ca13fa1fc4e/figures
2026-01-02 00:59:49.827221 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-02 00:59:49.832216 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-02 00:59:50.814281 INFO::Applying z-score to standardize continuous metadata
2026-01-02 00:59:50.822624 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-01-02 00:59:50.823612 INFO::Bypass z-score application to metadata
2026-01-02 00:59:50.826404 INFO::Bypass z-score application to metadata
2026-01-02 00:59:50.846345 INFO::Determining format of input files
2026-01-02 00:59:50.847358 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-02 00:59:50.848305 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-01-02 00:59:50.855959 INFO::Determining format of input files
2026-01-02 00:59:50.85703 INFO::Input format is data samples as columns and metadata samples as rows
2026-01-02 00:59:50.858343 INFO::Input format is feature_specific_covariate samples as columns
2026-01-02 00:59:50.866535 INFO::Determining format of input files
2026-01-02 00:59:50.867479 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-02 00:59:50.868535 INFO::Input format is feature_specific_covariate samples as columns
2026-01-02 00:59:50.870192 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-01-02 00:59:50.870993 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-01-02 00:59:50.882919 INFO::Running selected transform method: LOG
2026-01-02 00:59:50.88414 INFO::Creating output feature tables folder
2026-01-02 00:59:50.885045 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9Qceg7/file2d9ca154ecaaf/features/data_transformed.tsv
2026-01-02 00:59:50.888999 INFO::Running selected transform method: LOG
2026-01-02 00:59:50.890032 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9Qceg7/file2d9ca154ecaaf/features/data_transformed.tsv
2026-01-02 00:59:50.893772 INFO::Running selected transform method: PLOG
2026-01-02 00:59:50.895388 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9Qceg7/file2d9ca154ecaaf/features/data_transformed.tsv
2026-01-02 00:59:50.89828 INFO::Running selected transform method: NONE
2026-01-02 00:59:50.899047 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp9Qceg7/file2d9ca154ecaaf/features/data_transformed.tsv
2026-01-02 00:59:50.906851 INFO::Running the linear model component
2026-01-02 00:59:50.915558 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:50.919896 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:50.923957 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:50.931162 INFO::Counting total values for each feature
2026-01-02 00:59:50.932896 INFO::Running the logistic model component
2026-01-02 00:59:50.941621 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:50.947798 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:50.953839 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:50.962781 INFO::Counting total values for each feature
2026-01-02 00:59:50.964841 INFO::Re-running abundances for warn_prevalence
2026-01-02 00:59:50.965642 INFO::Running selected normalization method: TSS
2026-01-02 00:59:50.967068 INFO::Running selected transform method: LOG
2026-01-02 00:59:50.976138 INFO::Fitting model to feature number 1, a
2026-01-02 00:59:50.980868 INFO::Fitting model to feature number 2, b
2026-01-02 00:59:50.985341 INFO::Fitting model to feature number 3, c
2026-01-02 00:59:51.105227 INFO::Creating output folder
2026-01-02 00:59:51.106401 INFO::Creating fits folder
2026-01-02 00:59:51.107518 INFO::Writing residuals to file /tmp/Rtmp9Qceg7/file2d9ca17b7ca49e/fits/residuals_linear.rds
2026-01-02 00:59:51.108599 INFO::Writing fitted values to file /tmp/Rtmp9Qceg7/file2d9ca17b7ca49e/fits/fitted_linear.rds
2026-01-02 00:59:51.109798 INFO::Writing residuals to file /tmp/Rtmp9Qceg7/file2d9ca17b7ca49e/fits/residuals_logistic.rds
2026-01-02 00:59:51.111073 INFO::Writing fitted values to file /tmp/Rtmp9Qceg7/file2d9ca17b7ca49e/fits/fitted_logistic.rds
2026-01-02 00:59:51.114336 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp9Qceg7/file2d9ca17b7ca49e/all_results.tsv
2026-01-02 00:59:51.11621 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /tmp/Rtmp9Qceg7/file2d9ca17b7ca49e/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.120 5.334 367.423
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.529 | 0.732 | 20.264 | |
| maaslin_check_arguments | 0.159 | 0.004 | 0.163 | |
| maaslin_check_formula | 0.149 | 0.004 | 0.154 | |
| maaslin_compute_formula | 0.158 | 0.008 | 0.166 | |
| maaslin_contrast_test | 18.563 | 0.553 | 19.116 | |
| maaslin_filter | 0.452 | 0.007 | 0.458 | |
| maaslin_fit | 12.378 | 0.186 | 12.564 | |
| maaslin_log_arguments | 0.131 | 0.006 | 0.137 | |
| maaslin_normalize | 1.007 | 0.040 | 1.047 | |
| maaslin_plot_results | 43.064 | 0.370 | 43.412 | |
| maaslin_plot_results_from_output | 43.979 | 0.452 | 44.435 | |
| maaslin_process_metadata | 0.468 | 0.016 | 0.484 | |
| maaslin_read_data | 0.132 | 0.015 | 0.146 | |
| maaslin_reorder_data | 0.141 | 0.003 | 0.143 | |
| maaslin_transform | 0.548 | 0.037 | 0.585 | |
| maaslin_write_results | 13.030 | 0.143 | 13.175 | |
| maaslin_write_results_lefse_format | 15.569 | 0.083 | 15.652 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.005 | |