William Nickols
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-21 11:37 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 1154/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-11-21 00:58:39 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 01:20:17 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 1297.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results 42.826 0.383 43.163
maaslin_plot_results_from_output 42.743 0.330 43.078
maaslin3 20.005 0.608 20.621
maaslin_contrast_test 18.098 0.412 18.513
maaslin_write_results_lefse_format 14.827 0.041 14.868
maaslin_fit 13.288 0.092 13.381
maaslin_write_results 13.124 0.082 13.210
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-21 01:04:53.449643 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:04:53.527839 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:04:53.627169 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:04:53.650127 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:04:53.683962 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:04:53.766325 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:04:53.771538 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:04:53.78299 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:04:53.892131 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:04:53.89767 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:04:53.947822 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:04:53.988519 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:04:54.000564 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:04:54.039924 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:04:54.117759 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:05:10.106589 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:05:10.181975 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:05:10.256285 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:05:10.277919 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:05:10.311913 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:05:10.386286 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:05:10.391556 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:05:10.403135 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:05:10.509684 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:05:10.515109 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:05:10.56442 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:05:10.604395 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:05:10.616101 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:05:10.655718 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:05:10.72363 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:05:35.049934 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:05:35.129731 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:05:35.209314 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:05:35.234096 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:05:35.273021 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:05:35.355157 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:05:35.361106 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:05:35.373861 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:05:35.478774 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:05:35.484898 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:05:35.542291 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:05:35.587617 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:05:35.600564 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:05:35.658724 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:05:35.729954 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:05:48.041238 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:05:48.116693 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:05:48.190995 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:05:48.212659 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:05:48.24682 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:05:48.32512 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:05:48.330835 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:05:48.343072 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:05:48.445196 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:05:48.45086 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:05:48.50187 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:05:48.542953 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:05:48.555182 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:05:48.598434 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:05:48.690087 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:05:48.895273 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/residuals_linear.rds
2025-11-21 01:05:48.957006 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/fitted_linear.rds
2025-11-21 01:05:49.020952 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/residuals_logistic.rds
2025-11-21 01:05:49.325657 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/fitted_logistic.rds
2025-11-21 01:06:11.923798 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:06:12.001439 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:06:12.078192 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:06:12.102471 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:06:12.143022 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:06:12.230395 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:06:12.236454 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:06:12.249813 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:06:12.360698 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:06:12.366869 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:06:12.425043 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:06:12.473718 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:06:12.487474 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:06:12.534707 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:06:12.61622 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:06:24.732878 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:06:24.807868 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:06:24.882416 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:06:24.904403 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:06:24.938764 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:06:25.015701 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:06:25.021145 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:06:25.033027 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:06:25.130529 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:06:25.136212 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:06:25.19522 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:06:25.23563 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:06:25.247503 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:06:25.288692 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:06:25.358093 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:06:25.570736 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/residuals_linear.rds
2025-11-21 01:06:25.632185 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/fitted_linear.rds
2025-11-21 01:06:25.695521 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/residuals_logistic.rds
2025-11-21 01:06:25.998752 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/fitted_logistic.rds
2025-11-21 01:06:47.341284 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:06:47.422123 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:06:47.526365 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:06:47.548985 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:06:47.583835 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:06:47.661215 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:06:47.66672 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:06:47.678927 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:06:47.779051 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:06:47.784694 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:06:47.835413 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:06:47.876589 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:06:47.888972 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:06:47.930313 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:06:47.999277 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:07:00.060866 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:07:00.140015 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:07:00.2429 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:07:00.265493 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:07:00.300658 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:07:00.380718 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:07:00.386299 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:07:00.398812 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:07:00.497659 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:07:00.503099 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:07:00.55341 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:07:00.595416 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:07:00.607739 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:07:00.649711 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:07:00.718926 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:07:00.923027 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/residuals_linear.rds
2025-11-21 01:07:00.983689 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/fitted_linear.rds
2025-11-21 01:07:01.046533 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/residuals_logistic.rds
2025-11-21 01:07:01.346236 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd177e89e23/fits/fitted_logistic.rds
2025-11-21 01:07:22.670526 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:07:22.748688 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:07:22.845256 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:07:22.867172 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:07:22.901529 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:07:22.976349 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:07:22.981676 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:07:22.993556 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:07:23.0882 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:07:23.093641 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:07:23.143683 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:07:23.18457 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:07:23.196604 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:07:23.238093 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:07:23.307348 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:07:36.572567 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:07:36.649465 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:07:36.751956 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:07:36.774984 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:07:36.812686 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:07:36.890544 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:07:36.896059 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:07:36.908322 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:07:37.001848 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:07:37.007181 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:07:37.055722 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:07:37.095199 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:07:37.106963 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:07:37.147547 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:07:37.214828 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:08:00.693319 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:08:10.704845 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:08:35.652213 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:08:45.391877 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:08:46.01651 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_linear.rds
2025-11-21 01:08:46.077838 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_linear.rds
2025-11-21 01:08:46.116373 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_logistic.rds
2025-11-21 01:08:46.185113 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_logistic.rds
2025-11-21 01:09:08.857076 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:09:15.183609 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:09:15.488155 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_linear.rds
2025-11-21 01:09:15.549592 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_linear.rds
2025-11-21 01:09:15.587967 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_logistic.rds
2025-11-21 01:09:15.656804 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_logistic.rds
2025-11-21 01:09:34.451575 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:09:40.449086 WARNING::Fitting problem for feature 124 returning NA
2025-11-21 01:09:40.810159 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_linear.rds
2025-11-21 01:09:40.872223 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_linear.rds
2025-11-21 01:09:40.910901 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_logistic.rds
2025-11-21 01:09:40.979852 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_logistic.rds
2025-11-21 01:09:58.974476 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:09:59.05725 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:09:59.140141 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:09:59.163489 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:09:59.199925 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:09:59.281432 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:09:59.287253 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:09:59.300056 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:09:59.427536 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:09:59.433315 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:09:59.485051 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:09:59.526269 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:09:59.538433 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:09:59.579969 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:09:59.650267 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:10:11.412396 WARNING::Fitting problem for feature 50 returning NA
2025-11-21 01:10:11.487412 WARNING::Fitting problem for feature 62 returning NA
2025-11-21 01:10:11.561116 WARNING::Fitting problem for feature 74 returning NA
2025-11-21 01:10:11.582424 WARNING::Fitting problem for feature 78 returning NA
2025-11-21 01:10:11.617237 WARNING::Fitting problem for feature 84 returning NA
2025-11-21 01:10:11.693762 WARNING::Fitting problem for feature 96 returning NA
2025-11-21 01:10:11.699359 WARNING::Fitting problem for feature 97 returning NA
2025-11-21 01:10:11.711524 WARNING::Fitting problem for feature 99 returning NA
2025-11-21 01:10:11.837823 WARNING::Fitting problem for feature 114 returning NA
2025-11-21 01:10:11.843384 WARNING::Fitting problem for feature 115 returning NA
2025-11-21 01:10:11.893865 WARNING::Fitting problem for feature 123 returning NA
2025-11-21 01:10:11.934348 WARNING::Fitting problem for feature 130 returning NA
2025-11-21 01:10:11.946213 WARNING::Fitting problem for feature 132 returning NA
2025-11-21 01:10:11.986514 WARNING::Fitting problem for feature 139 returning NA
2025-11-21 01:10:12.056629 WARNING::Fitting problem for feature 150 returning NA
2025-11-21 01:10:12.301208 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_linear.rds
2025-11-21 01:10:12.36205 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_linear.rds
2025-11-21 01:10:12.424968 WARNING::Deleting existing residuals file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/residuals_logistic.rds
2025-11-21 01:10:12.724127 WARNING::Deleting existing fitted file: /tmp/RtmpsooZNY/fileb8cd160e5c71b/fits/fitted_logistic.rds
2025-11-21 01:10:32.839109 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-21 01:10:32.856207 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-21 01:10:32.867511 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-21 01:10:32.919182 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-21 01:10:32.936076 ERROR::Effect name not found in metadata: d
2025-11-21 01:10:32.947685 ERROR::No user formula provided
2025-11-21 01:10:32.978544 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-21 01:10:32.990281 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-21 01:10:36.981247 INFO::Writing function arguments to log file
2025-11-21 01:10:36.995116 INFO::Verifying options selected are valid
2025-11-21 01:10:39.264603 INFO::Writing function arguments to log file
2025-11-21 01:10:39.276997 INFO::Verifying options selected are valid
2025-11-21 01:10:39.278202 INFO::Determining format of input files
2025-11-21 01:10:39.279247 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-21 01:10:39.281718 INFO::Running selected normalization method: TSS
2025-11-21 01:10:39.283286 INFO::Creating output feature tables folder
2025-11-21 01:10:39.284321 INFO::Writing normalized data to file /tmp/RtmpsooZNY/fileb8cd1543697aa/features/data_norm.tsv
2025-11-21 01:10:39.285864 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-21 01:10:39.286873 INFO::Total samples in data: 16
2025-11-21 01:10:39.287763 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-21 01:10:39.288658 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-21 01:10:39.290658 INFO::Total filtered features: 0
2025-11-21 01:10:39.291667 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-21 01:10:39.292993 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-21 01:10:39.294009 INFO::Filtered feature names from variance filtering:
2025-11-21 01:10:39.294938 INFO::Writing filtered data to file /tmp/RtmpsooZNY/fileb8cd1543697aa/features/filtered_data.tsv
2025-11-21 01:10:39.296481 INFO::Running selected transform method: LOG
2025-11-21 01:10:39.297768 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsooZNY/fileb8cd1543697aa/features/data_transformed.tsv
2025-11-21 01:10:39.299537 INFO::Applying z-score to standardize continuous metadata
2025-11-21 01:10:39.30502 INFO::Running the linear model component
2025-11-21 01:10:39.318653 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:39.323159 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:39.327308 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:39.334522 INFO::Counting total values for each feature
2025-11-21 01:10:39.336439 INFO::Running the logistic model component
2025-11-21 01:10:39.361728 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:39.368119 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:39.374154 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:39.38289 INFO::Counting total values for each feature
2025-11-21 01:10:39.384996 INFO::Re-running abundances for warn_prevalence
2025-11-21 01:10:39.385917 INFO::Running selected normalization method: TSS
2025-11-21 01:10:39.387393 INFO::Running selected transform method: LOG
2025-11-21 01:10:39.400777 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:39.413745 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:39.418445 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:39.504949 INFO::Creating fits folder
2025-11-21 01:10:39.506154 INFO::Writing residuals to file /tmp/RtmpsooZNY/fileb8cd1543697aa/fits/residuals_linear.rds
2025-11-21 01:10:39.507314 INFO::Writing fitted values to file /tmp/RtmpsooZNY/fileb8cd1543697aa/fits/fitted_linear.rds
2025-11-21 01:10:39.50866 INFO::Writing residuals to file /tmp/RtmpsooZNY/fileb8cd1543697aa/fits/residuals_logistic.rds
2025-11-21 01:10:39.509964 INFO::Writing fitted values to file /tmp/RtmpsooZNY/fileb8cd1543697aa/fits/fitted_logistic.rds
2025-11-21 01:10:39.51272 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpsooZNY/fileb8cd1543697aa/all_results.tsv
2025-11-21 01:10:39.514431 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/RtmpsooZNY/fileb8cd1543697aa/significant_results.tsv
2025-11-21 01:10:39.515825 INFO::Creating output figures folder
2025-11-21 01:10:39.517271 INFO::Writing summary plot of significant
results to file: /tmp/RtmpsooZNY/fileb8cd1543697aa/figures/summary_plot.pdf
2025-11-21 01:10:41.157516 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpsooZNY/fileb8cd1543697aa/figures
2025-11-21 01:10:41.159546 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-21 01:10:41.164397 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-21 01:10:41.672061 INFO::Writing summary plot of
significant results to file: /tmp/RtmpsooZNY/fileb8cd1543697aa/figures/summary_plot.pdf
2025-11-21 01:10:43.222714 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpsooZNY/fileb8cd1543697aa/figures
2025-11-21 01:10:43.224353 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-21 01:10:43.229231 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-21 01:10:43.768377 INFO::Running the linear model component
2025-11-21 01:10:43.777095 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:43.78116 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:43.784925 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:43.791382 INFO::Counting total values for each feature
2025-11-21 01:10:43.792942 INFO::Running the logistic model component
2025-11-21 01:10:43.800845 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:43.806488 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:43.811915 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:43.820105 INFO::Counting total values for each feature
2025-11-21 01:10:43.822011 INFO::Re-running abundances for warn_prevalence
2025-11-21 01:10:43.822802 INFO::Running selected normalization method: TSS
2025-11-21 01:10:43.824143 INFO::Running selected transform method: LOG
2025-11-21 01:10:43.83224 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:43.836064 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:43.839676 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:43.921086 INFO::Creating output folder
2025-11-21 01:10:43.92206 INFO::Creating output figures folder
2025-11-21 01:10:43.923286 INFO::Writing summary plot of significant
results to file: /tmp/RtmpsooZNY/fileb8cd175865ba0/figures/summary_plot.pdf
2025-11-21 01:10:45.481841 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpsooZNY/fileb8cd175865ba0/figures
2025-11-21 01:10:45.483841 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-21 01:10:45.488982 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-21 01:10:46.455812 INFO::Applying z-score to standardize continuous metadata
2025-11-21 01:10:46.464194 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-21 01:10:46.465326 INFO::Bypass z-score application to metadata
2025-11-21 01:10:46.468453 INFO::Bypass z-score application to metadata
2025-11-21 01:10:46.489709 INFO::Determining format of input files
2025-11-21 01:10:46.490802 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-21 01:10:46.491703 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-21 01:10:46.499132 INFO::Determining format of input files
2025-11-21 01:10:46.50017 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-21 01:10:46.501476 INFO::Input format is feature_specific_covariate samples as columns
2025-11-21 01:10:46.50948 INFO::Determining format of input files
2025-11-21 01:10:46.510463 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-21 01:10:46.511561 INFO::Input format is feature_specific_covariate samples as columns
2025-11-21 01:10:46.513281 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-21 01:10:46.514113 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-21 01:10:46.526759 INFO::Running selected transform method: LOG
2025-11-21 01:10:46.528023 INFO::Creating output feature tables folder
2025-11-21 01:10:46.528946 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsooZNY/fileb8cd12b85c9bd/features/data_transformed.tsv
2025-11-21 01:10:46.532853 INFO::Running selected transform method: LOG
2025-11-21 01:10:46.533901 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsooZNY/fileb8cd12b85c9bd/features/data_transformed.tsv
2025-11-21 01:10:46.537648 INFO::Running selected transform method: PLOG
2025-11-21 01:10:46.539236 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsooZNY/fileb8cd12b85c9bd/features/data_transformed.tsv
2025-11-21 01:10:46.542161 INFO::Running selected transform method: NONE
2025-11-21 01:10:46.542951 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpsooZNY/fileb8cd12b85c9bd/features/data_transformed.tsv
2025-11-21 01:10:46.55116 INFO::Running the linear model component
2025-11-21 01:10:46.55985 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:46.56442 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:46.568562 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:46.575686 INFO::Counting total values for each feature
2025-11-21 01:10:46.577449 INFO::Running the logistic model component
2025-11-21 01:10:46.585743 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:46.592104 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:46.597816 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:46.606356 INFO::Counting total values for each feature
2025-11-21 01:10:46.6085 INFO::Re-running abundances for warn_prevalence
2025-11-21 01:10:46.609323 INFO::Running selected normalization method: TSS
2025-11-21 01:10:46.610681 INFO::Running selected transform method: LOG
2025-11-21 01:10:46.619074 INFO::Fitting model to feature number 1, a
2025-11-21 01:10:46.623147 INFO::Fitting model to feature number 2, b
2025-11-21 01:10:46.627001 INFO::Fitting model to feature number 3, c
2025-11-21 01:10:46.720016 INFO::Creating output folder
2025-11-21 01:10:46.721016 INFO::Creating fits folder
2025-11-21 01:10:46.721892 INFO::Writing residuals to file /tmp/RtmpsooZNY/fileb8cd169b1f2a1/fits/residuals_linear.rds
2025-11-21 01:10:46.722845 INFO::Writing fitted values to file /tmp/RtmpsooZNY/fileb8cd169b1f2a1/fits/fitted_linear.rds
2025-11-21 01:10:46.723984 INFO::Writing residuals to file /tmp/RtmpsooZNY/fileb8cd169b1f2a1/fits/residuals_logistic.rds
2025-11-21 01:10:46.725073 INFO::Writing fitted values to file /tmp/RtmpsooZNY/fileb8cd169b1f2a1/fits/fitted_logistic.rds
2025-11-21 01:10:46.727535 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpsooZNY/fileb8cd169b1f2a1/all_results.tsv
2025-11-21 01:10:46.729072 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/RtmpsooZNY/fileb8cd169b1f2a1/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
359.863 4.780 364.625
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.005 | 0.608 | 20.621 | |
| maaslin_check_arguments | 0.159 | 0.002 | 0.161 | |
| maaslin_check_formula | 0.135 | 0.005 | 0.140 | |
| maaslin_compute_formula | 0.160 | 0.006 | 0.166 | |
| maaslin_contrast_test | 18.098 | 0.412 | 18.513 | |
| maaslin_filter | 0.455 | 0.014 | 0.468 | |
| maaslin_fit | 13.288 | 0.092 | 13.381 | |
| maaslin_log_arguments | 0.125 | 0.005 | 0.129 | |
| maaslin_normalize | 0.257 | 0.005 | 0.262 | |
| maaslin_plot_results | 42.826 | 0.383 | 43.163 | |
| maaslin_plot_results_from_output | 42.743 | 0.330 | 43.078 | |
| maaslin_process_metadata | 0.434 | 0.018 | 0.452 | |
| maaslin_read_data | 0.124 | 0.001 | 0.125 | |
| maaslin_reorder_data | 0.127 | 0.003 | 0.130 | |
| maaslin_transform | 0.558 | 0.018 | 0.576 | |
| maaslin_write_results | 13.124 | 0.082 | 13.210 | |
| maaslin_write_results_lefse_format | 14.827 | 0.041 | 14.868 | |
| preprocess_dna_mtx | 0.002 | 0.002 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.001 | 0.004 | |