William Nickols
| Snapshot Date: 2026-02-20 13:45 -0500 (Fri, 20 Feb 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 2026-02-21 11:57 -0500 (Sat, 21 Feb 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" | 4890 |
| 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: 2026-02-21 00:58:34 -0500 (Sat, 21 Feb 2026) |
| EndedAt: 2026-02-21 01:20:18 -0500 (Sat, 21 Feb 2026) |
| EllapsedTime: 1304.5 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 43.954 0.175 44.101
maaslin_plot_results_from_output 43.054 0.355 43.413
maaslin3 20.462 0.525 20.988
maaslin_contrast_test 19.426 0.413 19.840
maaslin_write_results_lefse_format 14.720 0.231 14.953
maaslin_write_results 13.406 0.086 13.496
maaslin_fit 12.814 0.067 12.882
* 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")
2026-02-21 01:04:54.739033 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:04:54.838253 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:04:54.944278 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:04:54.966121 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:04:55.000209 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:04:55.076467 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:04:55.089146 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:04:55.101406 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:04:55.20011 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:04:55.205716 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:04:55.256405 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:04:55.303538 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:04:55.31521 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:04:55.355172 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:04:55.423687 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:05:11.305804 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:05:11.382074 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:05:11.458326 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:05:11.481331 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:05:11.516316 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:05:11.611519 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:05:11.617932 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:05:11.630941 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:05:11.727819 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:05:11.733338 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:05:11.787277 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:05:11.830703 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:05:11.843935 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:05:11.886065 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:05:11.955793 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:05:36.746209 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:05:36.826586 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:05:36.904031 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:05:36.926429 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:05:36.961388 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:05:37.038778 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:05:37.044213 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:05:37.056325 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:05:37.15619 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:05:37.162252 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:05:37.215282 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:05:37.259221 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:05:37.27252 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:05:37.31738 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:05:37.388714 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:05:50.335455 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:05:50.444965 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:05:50.524311 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:05:50.546602 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:05:50.58224 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:05:50.656861 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:05:50.662096 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:05:50.67373 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:05:50.766989 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:05:50.77238 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:05:50.821659 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:05:50.862149 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:05:50.874342 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:05:50.915864 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:05:50.986477 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:05:51.18944 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file38301947c3f115/fits/residuals_linear.rds
2026-02-21 01:05:51.251179 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file38301947c3f115/fits/fitted_linear.rds
2026-02-21 01:05:51.314174 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file38301947c3f115/fits/residuals_logistic.rds
2026-02-21 01:05:51.614771 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file38301947c3f115/fits/fitted_logistic.rds
2026-02-21 01:06:13.916299 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:06:14.017883 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:06:14.140188 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:06:14.162949 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:06:14.198913 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:06:14.279766 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:06:14.285445 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:06:14.298278 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:06:14.396167 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:06:14.401737 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:06:14.452898 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:06:14.493551 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:06:14.505951 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:06:14.546658 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:06:14.620027 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:06:27.089986 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:06:27.172967 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:06:27.255761 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:06:27.280178 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:06:27.318217 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:06:27.397468 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:06:27.403068 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:06:27.415431 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:06:27.518164 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:06:27.523836 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:06:27.574717 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:06:27.615303 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:06:27.627602 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:06:27.669713 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:06:27.741317 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:06:27.948755 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file38301947c3f115/fits/residuals_linear.rds
2026-02-21 01:06:28.009325 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file38301947c3f115/fits/fitted_linear.rds
2026-02-21 01:06:28.072102 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file38301947c3f115/fits/residuals_logistic.rds
2026-02-21 01:06:28.371193 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file38301947c3f115/fits/fitted_logistic.rds
2026-02-21 01:06:49.964947 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:06:50.049731 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:06:50.130488 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:06:50.155067 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:06:50.193164 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:06:50.295187 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:06:50.300581 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:06:50.312531 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:06:50.409481 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:06:50.415155 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:06:50.466281 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:06:50.506668 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:06:50.518581 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:06:50.559024 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:06:50.628273 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:07:02.868551 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:07:02.944483 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:07:03.019088 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:07:03.041168 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:07:03.077821 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:07:03.155642 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:07:03.16129 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:07:03.173588 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:07:03.273048 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:07:03.278531 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:07:03.330201 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:07:03.373064 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:07:03.385519 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:07:03.427225 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:07:03.500296 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:07:03.704958 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file38301947c3f115/fits/residuals_linear.rds
2026-02-21 01:07:03.76576 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file38301947c3f115/fits/fitted_linear.rds
2026-02-21 01:07:03.828969 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file38301947c3f115/fits/residuals_logistic.rds
2026-02-21 01:07:04.128725 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file38301947c3f115/fits/fitted_logistic.rds
2026-02-21 01:07:26.01754 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:07:26.096925 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:07:26.177295 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:07:26.202514 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:07:26.241725 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:07:26.319041 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:07:26.324852 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:07:26.337498 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:07:26.438273 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:07:26.443962 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:07:26.497497 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:07:26.540857 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:07:26.553896 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:07:26.59817 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:07:26.674147 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:07:38.596106 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:07:38.674096 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:07:38.753588 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:07:38.777177 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:07:38.81408 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:07:38.897478 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:07:38.903186 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:07:38.916189 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:07:39.024056 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:07:39.030075 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:07:39.085489 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:07:39.133152 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:07:39.147676 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:07:39.197064 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:07:39.27873 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:08:05.872869 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:08:14.636456 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:08:40.001815 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:08:50.116616 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:08:50.765775 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_linear.rds
2026-02-21 01:08:50.827743 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_linear.rds
2026-02-21 01:08:50.866827 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_logistic.rds
2026-02-21 01:08:50.9359 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_logistic.rds
2026-02-21 01:09:14.084067 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:09:19.433029 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:09:19.747253 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_linear.rds
2026-02-21 01:09:19.809141 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_linear.rds
2026-02-21 01:09:19.847824 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_logistic.rds
2026-02-21 01:09:19.916928 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_logistic.rds
2026-02-21 01:09:39.459299 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:09:46.018169 WARNING::Fitting problem for feature 124 returning NA
2026-02-21 01:09:46.328902 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_linear.rds
2026-02-21 01:09:46.390539 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_linear.rds
2026-02-21 01:09:46.429286 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_logistic.rds
2026-02-21 01:09:46.498328 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_logistic.rds
2026-02-21 01:10:05.939626 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:10:06.021951 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:10:06.099248 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:10:06.122273 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:10:06.158362 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:10:06.239438 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:10:06.244985 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:10:06.257393 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:10:06.357718 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:10:06.363379 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:10:06.443162 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:10:06.485126 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:10:06.497377 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:10:06.551172 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:10:06.625348 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:10:17.554458 WARNING::Fitting problem for feature 50 returning NA
2026-02-21 01:10:17.633207 WARNING::Fitting problem for feature 62 returning NA
2026-02-21 01:10:17.709562 WARNING::Fitting problem for feature 74 returning NA
2026-02-21 01:10:17.732092 WARNING::Fitting problem for feature 78 returning NA
2026-02-21 01:10:17.766787 WARNING::Fitting problem for feature 84 returning NA
2026-02-21 01:10:17.842916 WARNING::Fitting problem for feature 96 returning NA
2026-02-21 01:10:17.848363 WARNING::Fitting problem for feature 97 returning NA
2026-02-21 01:10:17.860604 WARNING::Fitting problem for feature 99 returning NA
2026-02-21 01:10:17.95643 WARNING::Fitting problem for feature 114 returning NA
2026-02-21 01:10:17.961936 WARNING::Fitting problem for feature 115 returning NA
2026-02-21 01:10:18.012326 WARNING::Fitting problem for feature 123 returning NA
2026-02-21 01:10:18.052936 WARNING::Fitting problem for feature 130 returning NA
2026-02-21 01:10:18.064936 WARNING::Fitting problem for feature 132 returning NA
2026-02-21 01:10:18.105881 WARNING::Fitting problem for feature 139 returning NA
2026-02-21 01:10:18.175623 WARNING::Fitting problem for feature 150 returning NA
2026-02-21 01:10:18.464956 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_linear.rds
2026-02-21 01:10:18.526304 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_linear.rds
2026-02-21 01:10:18.589815 WARNING::Deleting existing residuals file: /tmp/RtmpstOWdc/file383019176fab88/fits/residuals_logistic.rds
2026-02-21 01:10:18.889011 WARNING::Deleting existing fitted file: /tmp/RtmpstOWdc/file383019176fab88/fits/fitted_logistic.rds
2026-02-21 01:10:40.124726 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-02-21 01:10:40.142002 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-02-21 01:10:40.153617 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-02-21 01:10:40.208159 ERROR::No fixed, group, or
ordered effects included in formula.
2026-02-21 01:10:40.226531 ERROR::Effect name not found in metadata: d
2026-02-21 01:10:40.239099 ERROR::No user formula provided
2026-02-21 01:10:40.271596 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-02-21 01:10:40.283568 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-02-21 01:10:43.196888 INFO::Writing function arguments to log file
2026-02-21 01:10:43.21149 INFO::Verifying options selected are valid
2026-02-21 01:10:45.595334 INFO::Writing function arguments to log file
2026-02-21 01:10:45.607249 INFO::Verifying options selected are valid
2026-02-21 01:10:45.608308 INFO::Determining format of input files
2026-02-21 01:10:45.609272 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-21 01:10:45.611566 INFO::Running selected normalization method: TSS
2026-02-21 01:10:45.612982 INFO::Creating output feature tables folder
2026-02-21 01:10:45.613932 INFO::Writing normalized data to file /tmp/RtmpstOWdc/file3830191b34ce67/features/data_norm.tsv
2026-02-21 01:10:45.615378 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-02-21 01:10:45.616245 INFO::Total samples in data: 16
2026-02-21 01:10:45.617096 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-02-21 01:10:45.617945 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-02-21 01:10:45.619832 INFO::Total filtered features: 0
2026-02-21 01:10:45.620767 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-02-21 01:10:45.621893 INFO::Total features filtered by non-zero variance filtering: 0
2026-02-21 01:10:45.622821 INFO::Filtered feature names from variance filtering:
2026-02-21 01:10:45.623674 INFO::Writing filtered data to file /tmp/RtmpstOWdc/file3830191b34ce67/features/filtered_data.tsv
2026-02-21 01:10:45.625185 INFO::Running selected transform method: LOG
2026-02-21 01:10:45.626445 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpstOWdc/file3830191b34ce67/features/data_transformed.tsv
2026-02-21 01:10:45.628156 INFO::Applying z-score to standardize continuous metadata
2026-02-21 01:10:45.632685 INFO::Running the linear model component
2026-02-21 01:10:45.646171 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:45.650639 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:45.655322 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:45.66253 INFO::Counting total values for each feature
2026-02-21 01:10:45.664351 INFO::Running the logistic model component
2026-02-21 01:10:45.677901 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:45.684428 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:45.6906 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:45.699878 INFO::Counting total values for each feature
2026-02-21 01:10:45.702168 INFO::Re-running abundances for warn_prevalence
2026-02-21 01:10:45.703134 INFO::Running selected normalization method: TSS
2026-02-21 01:10:45.704677 INFO::Running selected transform method: LOG
2026-02-21 01:10:45.718593 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:45.723125 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:45.727443 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:45.806417 INFO::Creating fits folder
2026-02-21 01:10:45.807663 INFO::Writing residuals to file /tmp/RtmpstOWdc/file3830191b34ce67/fits/residuals_linear.rds
2026-02-21 01:10:45.808839 INFO::Writing fitted values to file /tmp/RtmpstOWdc/file3830191b34ce67/fits/fitted_linear.rds
2026-02-21 01:10:45.810037 INFO::Writing residuals to file /tmp/RtmpstOWdc/file3830191b34ce67/fits/residuals_logistic.rds
2026-02-21 01:10:45.81125 INFO::Writing fitted values to file /tmp/RtmpstOWdc/file3830191b34ce67/fits/fitted_logistic.rds
2026-02-21 01:10:45.81369 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpstOWdc/file3830191b34ce67/all_results.tsv
2026-02-21 01:10:45.815317 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/RtmpstOWdc/file3830191b34ce67/significant_results.tsv
2026-02-21 01:10:45.816677 INFO::Creating output figures folder
2026-02-21 01:10:45.818018 INFO::Writing summary plot of significant
results to file: /tmp/RtmpstOWdc/file3830191b34ce67/figures/summary_plot.pdf
2026-02-21 01:10:47.439515 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpstOWdc/file3830191b34ce67/figures
2026-02-21 01:10:47.44144 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-21 01:10:47.446451 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-21 01:10:47.974258 INFO::Writing summary plot of
significant results to file: /tmp/RtmpstOWdc/file3830191b34ce67/figures/summary_plot.pdf
2026-02-21 01:10:49.701164 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpstOWdc/file3830191b34ce67/figures
2026-02-21 01:10:49.702743 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-21 01:10:49.707858 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-21 01:10:50.248074 INFO::Running the linear model component
2026-02-21 01:10:50.257422 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:50.261773 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:50.265856 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:50.272901 INFO::Counting total values for each feature
2026-02-21 01:10:50.274559 INFO::Running the logistic model component
2026-02-21 01:10:50.283399 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:50.289776 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:50.295782 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:50.304784 INFO::Counting total values for each feature
2026-02-21 01:10:50.306929 INFO::Re-running abundances for warn_prevalence
2026-02-21 01:10:50.307773 INFO::Running selected normalization method: TSS
2026-02-21 01:10:50.309164 INFO::Running selected transform method: LOG
2026-02-21 01:10:50.318191 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:50.322547 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:50.326762 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:50.403476 INFO::Creating output folder
2026-02-21 01:10:50.404477 INFO::Creating output figures folder
2026-02-21 01:10:50.405771 INFO::Writing summary plot of significant
results to file: /tmp/RtmpstOWdc/file38301950d61c23/figures/summary_plot.pdf
2026-02-21 01:10:52.037995 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpstOWdc/file38301950d61c23/figures
2026-02-21 01:10:52.039742 INFO::Plotting associations from most to least significant, grouped by metadata
2026-02-21 01:10:52.044834 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-02-21 01:10:53.024279 INFO::Applying z-score to standardize continuous metadata
2026-02-21 01:10:53.031687 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-02-21 01:10:53.032598 INFO::Bypass z-score application to metadata
2026-02-21 01:10:53.035263 INFO::Bypass z-score application to metadata
2026-02-21 01:10:53.065745 INFO::Determining format of input files
2026-02-21 01:10:53.067719 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-21 01:10:53.068881 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-02-21 01:10:53.078784 INFO::Determining format of input files
2026-02-21 01:10:53.079833 INFO::Input format is data samples as columns and metadata samples as rows
2026-02-21 01:10:53.081216 INFO::Input format is feature_specific_covariate samples as columns
2026-02-21 01:10:53.090151 INFO::Determining format of input files
2026-02-21 01:10:53.091116 INFO::Input format is data samples as rows and metadata samples as rows
2026-02-21 01:10:53.092153 INFO::Input format is feature_specific_covariate samples as columns
2026-02-21 01:10:53.093859 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-02-21 01:10:53.094665 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-02-21 01:10:53.107098 INFO::Running selected transform method: LOG
2026-02-21 01:10:53.108278 INFO::Creating output feature tables folder
2026-02-21 01:10:53.109167 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpstOWdc/file38301957b2a34b/features/data_transformed.tsv
2026-02-21 01:10:53.113184 INFO::Running selected transform method: LOG
2026-02-21 01:10:53.114235 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpstOWdc/file38301957b2a34b/features/data_transformed.tsv
2026-02-21 01:10:53.118361 INFO::Running selected transform method: PLOG
2026-02-21 01:10:53.11996 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpstOWdc/file38301957b2a34b/features/data_transformed.tsv
2026-02-21 01:10:53.122989 INFO::Running selected transform method: NONE
2026-02-21 01:10:53.123745 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpstOWdc/file38301957b2a34b/features/data_transformed.tsv
2026-02-21 01:10:53.131395 INFO::Running the linear model component
2026-02-21 01:10:53.1398 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:53.143964 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:53.147881 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:53.154647 INFO::Counting total values for each feature
2026-02-21 01:10:53.156229 INFO::Running the logistic model component
2026-02-21 01:10:53.164374 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:53.170383 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:53.175989 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:53.184652 INFO::Counting total values for each feature
2026-02-21 01:10:53.186627 INFO::Re-running abundances for warn_prevalence
2026-02-21 01:10:53.18738 INFO::Running selected normalization method: TSS
2026-02-21 01:10:53.188692 INFO::Running selected transform method: LOG
2026-02-21 01:10:53.197086 INFO::Fitting model to feature number 1, a
2026-02-21 01:10:53.201425 INFO::Fitting model to feature number 2, b
2026-02-21 01:10:53.205702 INFO::Fitting model to feature number 3, c
2026-02-21 01:10:53.280446 INFO::Creating output folder
2026-02-21 01:10:53.281398 INFO::Creating fits folder
2026-02-21 01:10:53.282228 INFO::Writing residuals to file /tmp/RtmpstOWdc/file383019352cb168/fits/residuals_linear.rds
2026-02-21 01:10:53.283188 INFO::Writing fitted values to file /tmp/RtmpstOWdc/file383019352cb168/fits/fitted_linear.rds
2026-02-21 01:10:53.28422 INFO::Writing residuals to file /tmp/RtmpstOWdc/file383019352cb168/fits/residuals_logistic.rds
2026-02-21 01:10:53.285229 INFO::Writing fitted values to file /tmp/RtmpstOWdc/file383019352cb168/fits/fitted_logistic.rds
2026-02-21 01:10:53.287364 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpstOWdc/file383019352cb168/all_results.tsv
2026-02-21 01:10:53.28886 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/RtmpstOWdc/file383019352cb168/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
364.558 5.326 369.906
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.462 | 0.525 | 20.988 | |
| maaslin_check_arguments | 0.154 | 0.001 | 0.155 | |
| maaslin_check_formula | 0.181 | 0.000 | 0.180 | |
| maaslin_compute_formula | 0.149 | 0.001 | 0.150 | |
| maaslin_contrast_test | 19.426 | 0.413 | 19.840 | |
| maaslin_filter | 0.449 | 0.008 | 0.457 | |
| maaslin_fit | 12.814 | 0.067 | 12.882 | |
| maaslin_log_arguments | 0.131 | 0.001 | 0.133 | |
| maaslin_normalize | 0.265 | 0.003 | 0.268 | |
| maaslin_plot_results | 43.954 | 0.175 | 44.101 | |
| maaslin_plot_results_from_output | 43.054 | 0.355 | 43.413 | |
| maaslin_process_metadata | 0.469 | 0.023 | 0.491 | |
| maaslin_read_data | 0.133 | 0.001 | 0.134 | |
| maaslin_reorder_data | 0.133 | 0.002 | 0.136 | |
| maaslin_transform | 0.555 | 0.020 | 0.577 | |
| maaslin_write_results | 13.406 | 0.086 | 13.496 | |
| maaslin_write_results_lefse_format | 14.720 | 0.231 | 14.953 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.004 | 0.000 | 0.004 | |