William Nickols
| Snapshot Date: 2026-03-03 13:45 -0500 (Tue, 03 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-04 11:57 -0500 (Wed, 04 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: 2026-03-04 01:02:52 -0500 (Wed, 04 Mar 2026) |
| EndedAt: 2026-03-04 01:24:46 -0500 (Wed, 04 Mar 2026) |
| EllapsedTime: 1314.3 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_from_output 44.953 0.496 45.457
maaslin_plot_results 43.969 0.306 44.241
maaslin3 20.908 0.873 21.785
maaslin_contrast_test 19.138 0.382 19.524
maaslin_write_results_lefse_format 15.606 0.670 16.279
maaslin_write_results 15.055 0.965 16.021
maaslin_fit 12.836 0.184 13.023
* 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")
2026-03-04 01:09:18.838965 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:09:18.927971 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:09:19.021215 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:09:19.042849 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:09:19.076713 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:09:19.151256 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:09:19.163696 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:09:19.175527 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:09:19.268826 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:09:19.274206 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:09:19.323433 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:09:19.370121 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:09:19.382035 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:09:19.42195 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:09:19.48976 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:09:35.404545 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:09:35.480658 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:09:35.554707 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:09:35.576303 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:09:35.611811 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:09:35.706378 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:09:35.712043 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:09:35.723926 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:09:35.82092 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:09:35.826566 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:09:35.877666 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:09:35.920758 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:09:35.933118 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:09:35.974845 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:09:36.042752 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:10:00.798288 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:10:00.87906 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:10:00.95684 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:10:00.979837 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:10:01.016061 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:10:01.093222 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:10:01.106095 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:10:01.12 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:10:01.226753 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:10:01.232836 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:10:01.289392 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:10:01.335175 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:10:01.348634 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:10:01.394362 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:10:01.474716 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:10:14.55583 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:10:14.6598 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:10:14.733768 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:10:14.755587 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:10:14.789623 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:10:14.865658 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:10:14.871172 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:10:14.883219 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:10:14.979574 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:10:14.985063 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:10:15.035764 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:10:15.076389 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:10:15.088084 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:10:15.127666 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:10:15.195069 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:10:15.391986 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/residuals_linear.rds
2026-03-04 01:10:15.45362 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/fitted_linear.rds
2026-03-04 01:10:15.517515 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/residuals_logistic.rds
2026-03-04 01:10:15.823422 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/fitted_logistic.rds
2026-03-04 01:10:38.581716 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:10:38.664573 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:10:38.808566 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:10:38.833033 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:10:38.871148 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:10:38.954386 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:10:38.960139 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:10:38.972827 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:10:39.075827 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:10:39.082256 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:10:39.140425 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:10:39.187345 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:10:39.201129 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:10:39.245382 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:10:39.320771 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:10:51.585206 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:10:51.670851 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:10:51.752946 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:10:51.777739 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:10:51.816792 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:10:51.899885 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:10:51.90577 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:10:51.918435 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:10:52.023037 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:10:52.02891 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:10:52.081599 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:10:52.122516 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:10:52.134764 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:10:52.178159 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:10:52.251125 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:10:52.466404 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/residuals_linear.rds
2026-03-04 01:10:52.527879 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/fitted_linear.rds
2026-03-04 01:10:52.591159 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/residuals_logistic.rds
2026-03-04 01:10:52.890149 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/fitted_logistic.rds
2026-03-04 01:11:14.679632 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:11:14.761932 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:11:14.842449 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:11:14.866766 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:11:14.903798 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:11:15.020258 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:11:15.026011 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:11:15.038457 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:11:15.139378 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:11:15.145296 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:11:15.199352 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:11:15.241663 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:11:15.254449 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:11:15.297214 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:11:15.37445 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:11:27.547806 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:11:27.626451 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:11:27.705168 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:11:27.728381 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:11:27.765121 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:11:27.844873 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:11:27.850348 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:11:27.862258 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:11:27.961348 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:11:27.96716 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:11:28.020763 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:11:28.064571 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:11:28.077794 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:11:28.120799 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:11:28.196153 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:11:28.419434 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/residuals_linear.rds
2026-03-04 01:11:28.481605 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/fitted_linear.rds
2026-03-04 01:11:28.544644 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/residuals_logistic.rds
2026-03-04 01:11:28.842932 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d84332e9772ef/fits/fitted_logistic.rds
2026-03-04 01:11:50.323853 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:11:50.40208 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:11:50.481042 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:11:50.505271 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:11:50.540836 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:11:50.619215 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:11:50.625341 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:11:50.637879 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:11:50.739697 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:11:50.745523 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:11:50.799936 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:11:50.844865 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:11:50.85844 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:11:50.901004 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:11:50.973692 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:12:02.699688 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:12:02.77738 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:12:02.852199 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:12:02.875086 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:12:02.911832 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:12:02.990704 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:12:02.996099 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:12:03.008121 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:12:03.104269 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:12:03.109816 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:12:03.162109 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:12:03.205446 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:12:03.217891 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:12:03.259627 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:12:03.33142 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:12:29.706404 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:12:39.700968 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:13:04.430546 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:13:13.198789 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:13:13.844788 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_linear.rds
2026-03-04 01:13:13.906943 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_linear.rds
2026-03-04 01:13:13.945379 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_logistic.rds
2026-03-04 01:13:14.013937 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_logistic.rds
2026-03-04 01:13:36.758917 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:13:43.217194 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:13:43.51879 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_linear.rds
2026-03-04 01:13:43.58101 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_linear.rds
2026-03-04 01:13:43.619489 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_logistic.rds
2026-03-04 01:13:43.688608 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_logistic.rds
2026-03-04 01:14:02.360269 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:14:08.664337 WARNING::Fitting problem for feature 124 returning NA
2026-03-04 01:14:08.988636 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_linear.rds
2026-03-04 01:14:09.050033 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_linear.rds
2026-03-04 01:14:09.088578 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_logistic.rds
2026-03-04 01:14:09.157585 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_logistic.rds
2026-03-04 01:14:28.508617 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:14:28.588701 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:14:28.666288 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:14:28.689059 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:14:28.724691 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:14:28.802334 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:14:28.807765 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:14:28.819735 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:14:28.915718 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:14:28.92126 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:14:28.971983 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:14:29.013174 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:14:29.025288 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:14:29.066122 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:14:29.137228 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:14:40.149119 WARNING::Fitting problem for feature 50 returning NA
2026-03-04 01:14:40.226914 WARNING::Fitting problem for feature 62 returning NA
2026-03-04 01:14:40.302304 WARNING::Fitting problem for feature 74 returning NA
2026-03-04 01:14:40.32441 WARNING::Fitting problem for feature 78 returning NA
2026-03-04 01:14:40.35938 WARNING::Fitting problem for feature 84 returning NA
2026-03-04 01:14:40.437175 WARNING::Fitting problem for feature 96 returning NA
2026-03-04 01:14:40.442924 WARNING::Fitting problem for feature 97 returning NA
2026-03-04 01:14:40.455485 WARNING::Fitting problem for feature 99 returning NA
2026-03-04 01:14:40.558355 WARNING::Fitting problem for feature 114 returning NA
2026-03-04 01:14:40.564381 WARNING::Fitting problem for feature 115 returning NA
2026-03-04 01:14:40.618024 WARNING::Fitting problem for feature 123 returning NA
2026-03-04 01:14:40.662142 WARNING::Fitting problem for feature 130 returning NA
2026-03-04 01:14:40.674621 WARNING::Fitting problem for feature 132 returning NA
2026-03-04 01:14:40.715755 WARNING::Fitting problem for feature 139 returning NA
2026-03-04 01:14:40.786089 WARNING::Fitting problem for feature 150 returning NA
2026-03-04 01:14:41.177063 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_linear.rds
2026-03-04 01:14:41.238369 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_linear.rds
2026-03-04 01:14:41.301397 WARNING::Deleting existing residuals file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/residuals_logistic.rds
2026-03-04 01:14:41.601821 WARNING::Deleting existing fitted file: /tmp/RtmpbhM9Fi/file2d843337888c65/fits/fitted_logistic.rds
2026-03-04 01:15:02.37885 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-03-04 01:15:02.396255 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-03-04 01:15:02.40871 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-03-04 01:15:02.462185 ERROR::No fixed, group, or
ordered effects included in formula.
2026-03-04 01:15:02.478741 ERROR::Effect name not found in metadata: d
2026-03-04 01:15:02.489962 ERROR::No user formula provided
2026-03-04 01:15:02.521778 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-03-04 01:15:02.534433 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-03-04 01:15:05.509816 INFO::Writing function arguments to log file
2026-03-04 01:15:05.524044 INFO::Verifying options selected are valid
2026-03-04 01:15:07.898852 INFO::Writing function arguments to log file
2026-03-04 01:15:07.910798 INFO::Verifying options selected are valid
2026-03-04 01:15:07.911886 INFO::Determining format of input files
2026-03-04 01:15:07.912847 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 01:15:07.915096 INFO::Running selected normalization method: TSS
2026-03-04 01:15:07.916577 INFO::Creating output feature tables folder
2026-03-04 01:15:07.917626 INFO::Writing normalized data to file /tmp/RtmpbhM9Fi/file2d8433772aba97/features/data_norm.tsv
2026-03-04 01:15:07.919227 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-03-04 01:15:07.920202 INFO::Total samples in data: 16
2026-03-04 01:15:07.921133 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-03-04 01:15:07.922076 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-03-04 01:15:07.924272 INFO::Total filtered features: 0
2026-03-04 01:15:07.925348 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-03-04 01:15:07.926658 INFO::Total features filtered by non-zero variance filtering: 0
2026-03-04 01:15:07.927743 INFO::Filtered feature names from variance filtering:
2026-03-04 01:15:07.928766 INFO::Writing filtered data to file /tmp/RtmpbhM9Fi/file2d8433772aba97/features/filtered_data.tsv
2026-03-04 01:15:07.930527 INFO::Running selected transform method: LOG
2026-03-04 01:15:07.931918 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbhM9Fi/file2d8433772aba97/features/data_transformed.tsv
2026-03-04 01:15:07.933779 INFO::Applying z-score to standardize continuous metadata
2026-03-04 01:15:07.939201 INFO::Running the linear model component
2026-03-04 01:15:07.953857 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:07.958446 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:07.962669 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:07.969899 INFO::Counting total values for each feature
2026-03-04 01:15:07.971798 INFO::Running the logistic model component
2026-03-04 01:15:07.985577 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:07.992135 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:07.998281 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:08.007272 INFO::Counting total values for each feature
2026-03-04 01:15:08.009485 INFO::Re-running abundances for warn_prevalence
2026-03-04 01:15:08.01047 INFO::Running selected normalization method: TSS
2026-03-04 01:15:08.012031 INFO::Running selected transform method: LOG
2026-03-04 01:15:08.025958 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:08.030533 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:08.034914 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:08.136172 INFO::Creating fits folder
2026-03-04 01:15:08.137332 INFO::Writing residuals to file /tmp/RtmpbhM9Fi/file2d8433772aba97/fits/residuals_linear.rds
2026-03-04 01:15:08.138483 INFO::Writing fitted values to file /tmp/RtmpbhM9Fi/file2d8433772aba97/fits/fitted_linear.rds
2026-03-04 01:15:08.139628 INFO::Writing residuals to file /tmp/RtmpbhM9Fi/file2d8433772aba97/fits/residuals_logistic.rds
2026-03-04 01:15:08.140754 INFO::Writing fitted values to file /tmp/RtmpbhM9Fi/file2d8433772aba97/fits/fitted_logistic.rds
2026-03-04 01:15:08.143081 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpbhM9Fi/file2d8433772aba97/all_results.tsv
2026-03-04 01:15:08.144774 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/RtmpbhM9Fi/file2d8433772aba97/significant_results.tsv
2026-03-04 01:15:08.14613 INFO::Creating output figures folder
2026-03-04 01:15:08.147497 INFO::Writing summary plot of significant
results to file: /tmp/RtmpbhM9Fi/file2d8433772aba97/figures/summary_plot.pdf
2026-03-04 01:15:09.732521 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpbhM9Fi/file2d8433772aba97/figures
2026-03-04 01:15:09.734324 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-04 01:15:09.739276 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-04 01:15:10.261468 INFO::Writing summary plot of
significant results to file: /tmp/RtmpbhM9Fi/file2d8433772aba97/figures/summary_plot.pdf
2026-03-04 01:15:11.965196 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpbhM9Fi/file2d8433772aba97/figures
2026-03-04 01:15:11.966742 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-04 01:15:11.971638 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-04 01:15:12.502303 INFO::Running the linear model component
2026-03-04 01:15:12.511199 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:12.515464 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:12.519343 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:12.526257 INFO::Counting total values for each feature
2026-03-04 01:15:12.527899 INFO::Running the logistic model component
2026-03-04 01:15:12.536044 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:12.542032 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:12.547755 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:12.557127 INFO::Counting total values for each feature
2026-03-04 01:15:12.559611 INFO::Re-running abundances for warn_prevalence
2026-03-04 01:15:12.560558 INFO::Running selected normalization method: TSS
2026-03-04 01:15:12.562047 INFO::Running selected transform method: LOG
2026-03-04 01:15:12.570807 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:12.575056 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:12.579019 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:12.658413 INFO::Creating output folder
2026-03-04 01:15:12.659334 INFO::Creating output figures folder
2026-03-04 01:15:12.660544 INFO::Writing summary plot of significant
results to file: /tmp/RtmpbhM9Fi/file2d84332ed22d72/figures/summary_plot.pdf
2026-03-04 01:15:14.307716 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpbhM9Fi/file2d84332ed22d72/figures
2026-03-04 01:15:14.309273 INFO::Plotting associations from most to least significant, grouped by metadata
2026-03-04 01:15:14.313993 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-03-04 01:15:15.284055 INFO::Applying z-score to standardize continuous metadata
2026-03-04 01:15:15.291793 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-03-04 01:15:15.292752 INFO::Bypass z-score application to metadata
2026-03-04 01:15:15.29577 INFO::Bypass z-score application to metadata
2026-03-04 01:15:15.316406 INFO::Determining format of input files
2026-03-04 01:15:15.31741 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 01:15:15.318268 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-03-04 01:15:15.32631 INFO::Determining format of input files
2026-03-04 01:15:15.327419 INFO::Input format is data samples as columns and metadata samples as rows
2026-03-04 01:15:15.328764 INFO::Input format is feature_specific_covariate samples as columns
2026-03-04 01:15:15.337521 INFO::Determining format of input files
2026-03-04 01:15:15.338549 INFO::Input format is data samples as rows and metadata samples as rows
2026-03-04 01:15:15.339603 INFO::Input format is feature_specific_covariate samples as columns
2026-03-04 01:15:15.341256 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-03-04 01:15:15.342032 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-03-04 01:15:15.354017 INFO::Running selected transform method: LOG
2026-03-04 01:15:15.355246 INFO::Creating output feature tables folder
2026-03-04 01:15:15.356168 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbhM9Fi/file2d8433454a6a73/features/data_transformed.tsv
2026-03-04 01:15:15.360416 INFO::Running selected transform method: LOG
2026-03-04 01:15:15.361481 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbhM9Fi/file2d8433454a6a73/features/data_transformed.tsv
2026-03-04 01:15:15.365647 INFO::Running selected transform method: PLOG
2026-03-04 01:15:15.367356 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbhM9Fi/file2d8433454a6a73/features/data_transformed.tsv
2026-03-04 01:15:15.370548 INFO::Running selected transform method: NONE
2026-03-04 01:15:15.371323 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpbhM9Fi/file2d8433454a6a73/features/data_transformed.tsv
2026-03-04 01:15:15.379888 INFO::Running the linear model component
2026-03-04 01:15:15.389099 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:15.39397 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:15.398078 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:15.405238 INFO::Counting total values for each feature
2026-03-04 01:15:15.406915 INFO::Running the logistic model component
2026-03-04 01:15:15.41534 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:15.421781 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:15.427819 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:15.436758 INFO::Counting total values for each feature
2026-03-04 01:15:15.438852 INFO::Re-running abundances for warn_prevalence
2026-03-04 01:15:15.439725 INFO::Running selected normalization method: TSS
2026-03-04 01:15:15.441203 INFO::Running selected transform method: LOG
2026-03-04 01:15:15.45038 INFO::Fitting model to feature number 1, a
2026-03-04 01:15:15.455738 INFO::Fitting model to feature number 2, b
2026-03-04 01:15:15.460535 INFO::Fitting model to feature number 3, c
2026-03-04 01:15:15.541407 INFO::Creating output folder
2026-03-04 01:15:15.542408 INFO::Creating fits folder
2026-03-04 01:15:15.543247 INFO::Writing residuals to file /tmp/RtmpbhM9Fi/file2d84335adfb51a/fits/residuals_linear.rds
2026-03-04 01:15:15.544225 INFO::Writing fitted values to file /tmp/RtmpbhM9Fi/file2d84335adfb51a/fits/fitted_linear.rds
2026-03-04 01:15:15.545233 INFO::Writing residuals to file /tmp/RtmpbhM9Fi/file2d84335adfb51a/fits/residuals_logistic.rds
2026-03-04 01:15:15.546242 INFO::Writing fitted values to file /tmp/RtmpbhM9Fi/file2d84335adfb51a/fits/fitted_logistic.rds
2026-03-04 01:15:15.548491 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpbhM9Fi/file2d84335adfb51a/all_results.tsv
2026-03-04 01:15:15.549958 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/RtmpbhM9Fi/file2d84335adfb51a/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
363.179 4.549 367.835
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.908 | 0.873 | 21.785 | |
| maaslin_check_arguments | 0.139 | 0.000 | 0.139 | |
| maaslin_check_formula | 0.163 | 0.001 | 0.164 | |
| maaslin_compute_formula | 0.149 | 0.013 | 0.162 | |
| maaslin_contrast_test | 19.138 | 0.382 | 19.524 | |
| maaslin_filter | 0.467 | 0.005 | 0.472 | |
| maaslin_fit | 12.836 | 0.184 | 13.023 | |
| maaslin_log_arguments | 0.129 | 0.001 | 0.131 | |
| maaslin_normalize | 0.267 | 0.002 | 0.269 | |
| maaslin_plot_results | 43.969 | 0.306 | 44.241 | |
| maaslin_plot_results_from_output | 44.953 | 0.496 | 45.457 | |
| maaslin_process_metadata | 0.539 | 0.071 | 0.611 | |
| maaslin_read_data | 0.148 | 0.005 | 0.154 | |
| maaslin_reorder_data | 0.140 | 0.004 | 0.143 | |
| maaslin_transform | 0.589 | 0.062 | 0.651 | |
| maaslin_write_results | 15.055 | 0.965 | 16.021 | |
| maaslin_write_results_lefse_format | 15.606 | 0.670 | 16.279 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.003 | |