William Nickols
| Snapshot Date: 2026-03-10 13:45 -0400 (Tue, 10 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-11 11:57 -0400 (Wed, 11 Mar 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" | 4892 |
| 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 | | ||||||||
| 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. |
| Package: maaslin3 |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2026-03-11 00:49:10 -0400 (Wed, 11 Mar 2026) |
| EndedAt: 2026-03-11 01:10:49 -0400 (Wed, 11 Mar 2026) |
| EllapsedTime: 1298.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.2.0’
* 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 44.201 0.409 44.579
maaslin_plot_results_from_output 43.456 0.392 43.855
maaslin3 20.594 0.499 21.095
maaslin_contrast_test 18.699 0.282 18.982
maaslin_write_results_lefse_format 14.750 0.093 14.847
maaslin_write_results 13.669 0.237 13.909
maaslin_fit 12.698 0.222 12.921
* 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-3.22-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2026-03-11 00:55:26.514639 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:55:26.601447 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:55:26.698694 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:55:26.721226 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:55:26.756413 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:55:26.83177 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:55:26.844163 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:55:26.856081 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:55:26.94968 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:55:26.95535 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:55:27.006038 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:55:27.054165 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:55:27.065801 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:55:27.106407 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:55:27.174563 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:55:42.850818 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:55:42.924238 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:55:42.998149 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:55:43.019261 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:55:43.052475 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:55:43.139722 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:55:43.145242 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:55:43.157112 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:55:43.252532 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:55:43.257927 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:55:43.307304 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:55:43.348137 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:55:43.360122 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:55:43.40064 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:55:43.467926 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:56:07.91171 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:56:07.994859 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:56:08.074378 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:56:08.097366 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:56:08.132636 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:56:08.209891 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:56:08.215497 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:56:08.227702 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:56:08.326589 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:56:08.332429 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:56:08.383524 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:56:08.425124 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:56:08.437753 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:56:08.480773 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:56:08.555892 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:56:21.478907 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:56:21.578173 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:56:21.649759 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:56:21.670555 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:56:21.704086 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:56:21.778306 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:56:21.783604 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:56:21.795193 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:56:21.887504 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:56:21.892886 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:56:21.940803 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:56:21.980252 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:56:21.992182 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:56:22.031943 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:56:22.100061 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:56:22.30165 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/residuals_linear.rds
2026-03-11 00:56:22.363936 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/fitted_linear.rds
2026-03-11 00:56:22.431556 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/residuals_logistic.rds
2026-03-11 00:56:22.735269 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/fitted_logistic.rds
2026-03-11 00:56:44.943444 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:56:45.023855 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:56:45.13221 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:56:45.153811 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:56:45.188159 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:56:45.2653 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:56:45.270969 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:56:45.283292 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:56:45.380471 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:56:45.386118 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:56:45.436901 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:56:45.476522 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:56:45.488132 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:56:45.527754 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:56:45.595824 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:56:57.533247 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:56:57.615774 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:56:57.69459 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:56:57.718005 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:56:57.755408 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:56:57.833681 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:56:57.839185 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:56:57.851437 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:56:57.950162 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:56:57.955825 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:56:58.006717 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:56:58.048351 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:56:58.060756 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:56:58.102544 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:56:58.173087 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:56:58.375376 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/residuals_linear.rds
2026-03-11 00:56:58.436493 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/fitted_linear.rds
2026-03-11 00:56:58.499461 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/residuals_logistic.rds
2026-03-11 00:56:58.798778 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/fitted_logistic.rds
2026-03-11 00:57:20.441882 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:57:20.524614 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:57:20.605733 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:57:20.630824 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:57:20.669772 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:57:20.778204 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:57:20.78404 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:57:20.79782 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:57:20.898814 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:57:20.90434 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:57:20.954771 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:57:20.996032 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:57:21.008337 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:57:21.051125 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:57:21.123854 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:57:33.132702 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:57:33.20927 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:57:33.285513 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:57:33.307662 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:57:33.342836 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:57:33.41981 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:57:33.425362 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:57:33.4373 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:57:33.534047 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:57:33.539644 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:57:33.58921 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:57:33.630454 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:57:33.642702 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:57:33.68485 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:57:33.757636 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:57:33.966666 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/residuals_linear.rds
2026-03-11 00:57:34.028645 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/fitted_linear.rds
2026-03-11 00:57:34.092414 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/residuals_logistic.rds
2026-03-11 00:57:34.393929 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d471dd6ad/fits/fitted_logistic.rds
2026-03-11 00:57:55.944751 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:57:56.02161 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:57:56.099503 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:57:56.121574 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:57:56.156424 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:57:56.234854 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:57:56.240829 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:57:56.25342 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:57:56.353596 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:57:56.359383 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:57:56.413166 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:57:56.457608 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:57:56.471157 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:57:56.516893 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:57:56.597946 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:58:08.166992 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 00:58:08.243792 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 00:58:08.318567 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 00:58:08.340974 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 00:58:08.377048 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 00:58:08.455455 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 00:58:08.460888 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 00:58:08.47308 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 00:58:08.570439 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 00:58:08.576387 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 00:58:08.630242 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 00:58:08.67119 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 00:58:08.683225 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 00:58:08.7247 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 00:58:08.796899 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 00:58:32.83182 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 00:58:42.882631 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 00:59:07.680827 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 00:59:17.399448 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 00:59:18.016757 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_linear.rds
2026-03-11 00:59:18.078556 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_linear.rds
2026-03-11 00:59:18.117325 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_logistic.rds
2026-03-11 00:59:18.186345 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_logistic.rds
2026-03-11 00:59:41.778794 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 00:59:48.09165 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 00:59:48.405294 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_linear.rds
2026-03-11 00:59:48.468925 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_linear.rds
2026-03-11 00:59:48.5085 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_logistic.rds
2026-03-11 00:59:48.580204 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_logistic.rds
2026-03-11 01:00:07.161394 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 01:00:13.503143 WARNING::Fitting problem for feature 124 returning NA
2026-03-11 01:00:13.830863 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_linear.rds
2026-03-11 01:00:13.892792 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_linear.rds
2026-03-11 01:00:13.931529 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_logistic.rds
2026-03-11 01:00:14.000355 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_logistic.rds
2026-03-11 01:00:32.361866 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 01:00:32.443459 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 01:00:32.525581 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 01:00:32.550063 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 01:00:32.589234 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 01:00:32.71692 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 01:00:32.723224 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 01:00:32.736707 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 01:00:32.84188 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 01:00:32.8481 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 01:00:32.902663 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 01:00:32.944901 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 01:00:32.957264 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 01:00:33.000698 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 01:00:33.07409 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 01:00:44.878625 WARNING::Fitting problem for feature 50 returning NA
2026-03-11 01:00:44.958918 WARNING::Fitting problem for feature 62 returning NA
2026-03-11 01:00:45.038665 WARNING::Fitting problem for feature 74 returning NA
2026-03-11 01:00:45.063911 WARNING::Fitting problem for feature 78 returning NA
2026-03-11 01:00:45.10137 WARNING::Fitting problem for feature 84 returning NA
2026-03-11 01:00:45.181179 WARNING::Fitting problem for feature 96 returning NA
2026-03-11 01:00:45.186899 WARNING::Fitting problem for feature 97 returning NA
2026-03-11 01:00:45.199525 WARNING::Fitting problem for feature 99 returning NA
2026-03-11 01:00:45.303539 WARNING::Fitting problem for feature 114 returning NA
2026-03-11 01:00:45.310323 WARNING::Fitting problem for feature 115 returning NA
2026-03-11 01:00:45.365522 WARNING::Fitting problem for feature 123 returning NA
2026-03-11 01:00:45.408728 WARNING::Fitting problem for feature 130 returning NA
2026-03-11 01:00:45.421858 WARNING::Fitting problem for feature 132 returning NA
2026-03-11 01:00:45.463475 WARNING::Fitting problem for feature 139 returning NA
2026-03-11 01:00:45.567064 WARNING::Fitting problem for feature 150 returning NA
2026-03-11 01:00:45.803277 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_linear.rds
2026-03-11 01:00:45.864454 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_linear.rds
2026-03-11 01:00:45.92782 WARNING::Deleting existing residuals file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/residuals_logistic.rds
2026-03-11 01:00:46.226974 WARNING::Deleting existing fitted file: /tmp/Rtmp4eCto5/file3e3a6d3f180778/fits/fitted_logistic.rds
2026-03-11 01:01:07.71775 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-11 01:01:07.736496 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-11 01:01:07.74933 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-11 01:01:07.809998 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-11 01:01:07.828357 ERROR::Effect name not found in metadata: d
2026-03-11 01:01:07.841821 ERROR::No user formula provided
2026-03-11 01:01:07.873542 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-11 01:01:07.885222 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-11 01:01:10.678527 INFO::Writing function arguments to log file
2026-03-11 01:01:10.692892 INFO::Verifying options selected are valid
2026-03-11 01:01:13.049749 INFO::Writing function arguments to log file
2026-03-11 01:01:13.061985 INFO::Verifying options selected are valid
2026-03-11 01:01:13.063072 INFO::Determining format of input files
2026-03-11 01:01:13.064024 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-11 01:01:13.066337 INFO::Running selected normalization method: TSS
2026-03-11 01:01:13.067818 INFO::Creating output feature tables folder
2026-03-11 01:01:13.06879 INFO::Writing normalized data to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/features/data_norm.tsv
2026-03-11 01:01:13.070277 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-11 01:01:13.071162 INFO::Total samples in data: 16
2026-03-11 01:01:13.072017 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-11 01:01:13.072871 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-11 01:01:13.074768 INFO::Total filtered features: 0
2026-03-11 01:01:13.075725 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-11 01:01:13.076879 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-11 01:01:13.077824 INFO::Filtered feature names from variance filtering:
2026-03-11 01:01:13.078695 INFO::Writing filtered data to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/features/filtered_data.tsv
2026-03-11 01:01:13.080149 INFO::Running selected transform method: LOG
2026-03-11 01:01:13.08133 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/features/data_transformed.tsv
2026-03-11 01:01:13.082952 INFO::Applying z-score to standardize continuous metadata
2026-03-11 01:01:13.087446 INFO::Running the linear model component
2026-03-11 01:01:13.101377 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:13.105938 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:13.110277 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:13.117573 INFO::Counting total values for each feature
2026-03-11 01:01:13.119459 INFO::Running the logistic model component
2026-03-11 01:01:13.133368 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:13.139989 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:13.14612 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:13.155127 INFO::Counting total values for each feature
2026-03-11 01:01:13.157384 INFO::Re-running abundances for warn_prevalence
2026-03-11 01:01:13.158336 INFO::Running selected normalization method: TSS
2026-03-11 01:01:13.159838 INFO::Running selected transform method: LOG
2026-03-11 01:01:13.173968 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:13.178545 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:13.182794 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:13.26366 INFO::Creating fits folder
2026-03-11 01:01:13.26498 INFO::Writing residuals to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/fits/residuals_linear.rds
2026-03-11 01:01:13.266191 INFO::Writing fitted values to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/fits/fitted_linear.rds
2026-03-11 01:01:13.267412 INFO::Writing residuals to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/fits/residuals_logistic.rds
2026-03-11 01:01:13.268618 INFO::Writing fitted values to file /tmp/Rtmp4eCto5/file3e3a6d478edf76/fits/fitted_logistic.rds
2026-03-11 01:01:13.270993 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp4eCto5/file3e3a6d478edf76/all_results.tsv
2026-03-11 01:01:13.272671 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/Rtmp4eCto5/file3e3a6d478edf76/significant_results.tsv
2026-03-11 01:01:13.274021 INFO::Creating output figures folder
2026-03-11 01:01:13.275393 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp4eCto5/file3e3a6d478edf76/figures/summary_plot.pdf
2026-03-11 01:01:14.879256 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp4eCto5/file3e3a6d478edf76/figures
2026-03-11 01:01:14.881126 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-11 01:01:14.886149 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-11 01:01:15.422117 INFO::Writing summary plot of
significant results to file: /tmp/Rtmp4eCto5/file3e3a6d478edf76/figures/summary_plot.pdf
2026-03-11 01:01:17.009727 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp4eCto5/file3e3a6d478edf76/figures
2026-03-11 01:01:17.011321 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-11 01:01:17.016383 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-11 01:01:17.560712 INFO::Running the linear model component
2026-03-11 01:01:17.570874 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:17.575871 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:17.580453 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:17.588525 INFO::Counting total values for each feature
2026-03-11 01:01:17.590315 INFO::Running the logistic model component
2026-03-11 01:01:17.599182 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:17.606154 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:17.612809 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:17.622991 INFO::Counting total values for each feature
2026-03-11 01:01:17.625228 INFO::Re-running abundances for warn_prevalence
2026-03-11 01:01:17.626091 INFO::Running selected normalization method: TSS
2026-03-11 01:01:17.627526 INFO::Running selected transform method: LOG
2026-03-11 01:01:17.636704 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:17.64122 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:17.645436 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:17.726687 INFO::Creating output folder
2026-03-11 01:01:17.727705 INFO::Creating output figures folder
2026-03-11 01:01:17.728953 INFO::Writing summary plot of significant
results to file: /tmp/Rtmp4eCto5/file3e3a6d5620ca2a/figures/summary_plot.pdf
2026-03-11 01:01:19.372593 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp4eCto5/file3e3a6d5620ca2a/figures
2026-03-11 01:01:19.374267 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-11 01:01:19.379244 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-11 01:01:20.336495 INFO::Applying z-score to standardize continuous metadata
2026-03-11 01:01:20.344019 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-11 01:01:20.345022 INFO::Bypass z-score application to metadata
2026-03-11 01:01:20.347692 INFO::Bypass z-score application to metadata
2026-03-11 01:01:20.366645 INFO::Determining format of input files
2026-03-11 01:01:20.367591 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-11 01:01:20.368403 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-11 01:01:20.375621 INFO::Determining format of input files
2026-03-11 01:01:20.376601 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-11 01:01:20.377845 INFO::Input format is feature_specific_covariate samples as columns
2026-03-11 01:01:20.385794 INFO::Determining format of input files
2026-03-11 01:01:20.386728 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-11 01:01:20.387738 INFO::Input format is feature_specific_covariate samples as columns
2026-03-11 01:01:20.389351 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-11 01:01:20.390116 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-11 01:01:20.401728 INFO::Running selected transform method: LOG
2026-03-11 01:01:20.402972 INFO::Creating output feature tables folder
2026-03-11 01:01:20.403898 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4eCto5/file3e3a6d4a9cc1d3/features/data_transformed.tsv
2026-03-11 01:01:20.408331 INFO::Running selected transform method: LOG
2026-03-11 01:01:20.409457 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4eCto5/file3e3a6d4a9cc1d3/features/data_transformed.tsv
2026-03-11 01:01:20.413738 INFO::Running selected transform method: PLOG
2026-03-11 01:01:20.426154 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4eCto5/file3e3a6d4a9cc1d3/features/data_transformed.tsv
2026-03-11 01:01:20.429451 INFO::Running selected transform method: NONE
2026-03-11 01:01:20.430256 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp4eCto5/file3e3a6d4a9cc1d3/features/data_transformed.tsv
2026-03-11 01:01:20.438498 INFO::Running the linear model component
2026-03-11 01:01:20.447073 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:20.451303 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:20.455257 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:20.462033 INFO::Counting total values for each feature
2026-03-11 01:01:20.463648 INFO::Running the logistic model component
2026-03-11 01:01:20.472137 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:20.478266 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:20.484033 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:20.492631 INFO::Counting total values for each feature
2026-03-11 01:01:20.494583 INFO::Re-running abundances for warn_prevalence
2026-03-11 01:01:20.495324 INFO::Running selected normalization method: TSS
2026-03-11 01:01:20.49663 INFO::Running selected transform method: LOG
2026-03-11 01:01:20.50497 INFO::Fitting model to feature number 1, a
2026-03-11 01:01:20.509068 INFO::Fitting model to feature number 2, b
2026-03-11 01:01:20.512998 INFO::Fitting model to feature number 3, c
2026-03-11 01:01:20.588934 INFO::Creating output folder
2026-03-11 01:01:20.589947 INFO::Creating fits folder
2026-03-11 01:01:20.590779 INFO::Writing residuals to file /tmp/Rtmp4eCto5/file3e3a6d7d1bd32a/fits/residuals_linear.rds
2026-03-11 01:01:20.591742 INFO::Writing fitted values to file /tmp/Rtmp4eCto5/file3e3a6d7d1bd32a/fits/fitted_linear.rds
2026-03-11 01:01:20.592743 INFO::Writing residuals to file /tmp/Rtmp4eCto5/file3e3a6d7d1bd32a/fits/residuals_logistic.rds
2026-03-11 01:01:20.593737 INFO::Writing fitted values to file /tmp/Rtmp4eCto5/file3e3a6d7d1bd32a/fits/fitted_logistic.rds
2026-03-11 01:01:20.595936 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmp4eCto5/file3e3a6d7d1bd32a/all_results.tsv
2026-03-11 01:01:20.597391 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/Rtmp4eCto5/file3e3a6d7d1bd32a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
360.619 4.556 365.162
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.594 | 0.499 | 21.095 | |
| maaslin_check_arguments | 0.139 | 0.001 | 0.140 | |
| maaslin_check_formula | 0.137 | 0.000 | 0.137 | |
| maaslin_compute_formula | 0.167 | 0.001 | 0.168 | |
| maaslin_contrast_test | 18.699 | 0.282 | 18.982 | |
| maaslin_filter | 0.421 | 0.009 | 0.430 | |
| maaslin_fit | 12.698 | 0.222 | 12.921 | |
| maaslin_log_arguments | 0.130 | 0.001 | 0.132 | |
| maaslin_normalize | 0.264 | 0.005 | 0.270 | |
| maaslin_plot_results | 44.201 | 0.409 | 44.579 | |
| maaslin_plot_results_from_output | 43.456 | 0.392 | 43.855 | |
| maaslin_process_metadata | 0.433 | 0.008 | 0.441 | |
| maaslin_read_data | 0.127 | 0.000 | 0.126 | |
| maaslin_reorder_data | 0.129 | 0.002 | 0.130 | |
| maaslin_transform | 0.528 | 0.010 | 0.538 | |
| maaslin_write_results | 13.669 | 0.237 | 13.909 | |
| maaslin_write_results_lefse_format | 14.750 | 0.093 | 14.847 | |
| preprocess_dna_mtx | 0.003 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |