William Nickols
| Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 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 2025-11-22 11:37 -0500 (Sat, 22 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" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4567 |
| 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: 2025-11-22 00:57:21 -0500 (Sat, 22 Nov 2025) |
| EndedAt: 2025-11-22 01:19:10 -0500 (Sat, 22 Nov 2025) |
| EllapsedTime: 1308.8 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 42.633 0.445 43.039
maaslin_plot_results_from_output 42.567 0.348 42.924
maaslin3 20.150 0.553 20.707
maaslin_contrast_test 18.202 0.448 18.658
maaslin_write_results_lefse_format 14.184 0.127 14.313
maaslin_write_results 13.709 0.222 13.932
maaslin_fit 12.602 0.081 12.683
* 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")
2025-11-22 01:03:37.384108 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:03:37.458621 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:03:37.548455 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:03:37.569815 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:03:37.603625 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:03:37.683627 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:03:37.688834 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:03:37.700271 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:03:37.808338 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:03:37.813676 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:03:37.86222 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:03:37.901966 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:03:37.913631 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:03:37.954005 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:03:38.028047 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:03:53.438973 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:03:53.517769 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:03:53.59273 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:03:53.614049 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:03:53.647457 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:03:53.722198 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:03:53.727539 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:03:53.739524 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:03:53.850273 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:03:53.855904 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:03:53.90512 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:03:53.946163 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:03:53.957883 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:03:53.998305 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:03:54.067766 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:04:18.286076 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:04:18.360835 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:04:18.435149 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:04:18.456648 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:04:18.490699 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:04:18.566883 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:04:18.572821 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:04:18.585044 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:04:18.682326 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:04:18.687763 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:04:18.737744 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:04:18.778674 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:04:18.790638 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:04:18.849564 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:04:18.917474 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:04:31.490525 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:04:31.565146 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:04:31.639603 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:04:31.660723 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:04:31.694265 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:04:31.769926 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:04:31.775493 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:04:31.787816 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:04:31.884083 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:04:31.889423 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:04:31.938025 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:04:31.976762 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:04:31.988556 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:04:32.028456 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:04:32.1166 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:04:32.316515 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/residuals_linear.rds
2025-11-22 01:04:32.378127 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/fitted_linear.rds
2025-11-22 01:04:32.441907 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/residuals_logistic.rds
2025-11-22 01:04:32.741965 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/fitted_logistic.rds
2025-11-22 01:04:55.159641 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:04:55.236314 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:04:55.312926 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:04:55.337824 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:04:55.378763 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:04:55.467505 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:04:55.473808 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:04:55.487951 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:04:55.599315 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:04:55.605424 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:04:55.662926 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:04:55.709187 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:04:55.722799 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:04:55.768681 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:04:55.849293 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:05:07.752702 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:05:07.829252 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:05:07.905229 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:05:07.92721 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:05:07.961957 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:05:08.043139 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:05:08.048826 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:05:08.061327 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:05:08.163065 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:05:08.168975 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:05:08.22073 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:05:08.261637 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:05:08.273565 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:05:08.31584 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:05:08.38625 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:05:08.602142 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/residuals_linear.rds
2025-11-22 01:05:08.663269 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/fitted_linear.rds
2025-11-22 01:05:08.726574 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/residuals_logistic.rds
2025-11-22 01:05:09.026328 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/fitted_logistic.rds
2025-11-22 01:05:30.526875 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:05:30.627861 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:05:30.746253 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:05:30.772121 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:05:30.814722 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:05:30.902338 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:05:30.908263 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:05:30.921093 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:05:31.02691 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:05:31.033027 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:05:31.088093 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:05:31.134793 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:05:31.149479 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:05:31.193564 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:05:31.270418 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:05:43.155325 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:05:43.233511 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:05:43.339203 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:05:43.362959 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:05:43.400044 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:05:43.484246 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:05:43.489608 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:05:43.501644 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:05:43.599475 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:05:43.605144 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:05:43.658517 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:05:43.699326 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:05:43.71111 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:05:43.751632 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:05:43.823297 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:05:44.039947 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/residuals_linear.rds
2025-11-22 01:05:44.101138 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/fitted_linear.rds
2025-11-22 01:05:44.16473 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/residuals_logistic.rds
2025-11-22 01:05:44.466409 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e6355ffc5/fits/fitted_logistic.rds
2025-11-22 01:06:06.092474 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:06:06.180851 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:06:06.286318 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:06:06.310282 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:06:06.346227 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:06:06.423702 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:06:06.429165 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:06:06.440962 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:06:06.538155 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:06:06.543817 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:06:06.595045 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:06:06.635173 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:06:06.647224 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:06:06.688439 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:06:06.758247 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:06:18.800905 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:06:18.880456 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:06:18.957839 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:06:18.980722 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:06:19.015431 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:06:19.092997 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:06:19.098823 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:06:19.111673 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:06:19.241922 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:06:19.247506 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:06:19.298955 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:06:19.339368 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:06:19.351522 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:06:19.391974 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:06:19.463514 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:06:44.260282 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:06:53.247426 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:07:20.266365 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:07:29.252948 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:07:29.927737 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_linear.rds
2025-11-22 01:07:29.989486 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_linear.rds
2025-11-22 01:07:30.028156 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_logistic.rds
2025-11-22 01:07:30.097234 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_logistic.rds
2025-11-22 01:07:53.321686 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:07:59.698658 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:08:00.027798 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_linear.rds
2025-11-22 01:08:00.089894 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_linear.rds
2025-11-22 01:08:00.128713 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_logistic.rds
2025-11-22 01:08:00.200127 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_logistic.rds
2025-11-22 01:08:19.23014 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:08:25.370227 WARNING::Fitting problem for feature 124 returning NA
2025-11-22 01:08:25.683854 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_linear.rds
2025-11-22 01:08:25.746248 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_linear.rds
2025-11-22 01:08:25.785506 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_logistic.rds
2025-11-22 01:08:25.856995 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_logistic.rds
2025-11-22 01:08:44.105926 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:08:44.184068 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:08:44.261285 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:08:44.28388 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:08:44.320665 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:08:44.410175 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:08:44.417398 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:08:44.430713 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:08:44.531179 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:08:44.537002 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:08:44.590926 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:08:44.635418 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:08:44.648532 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:08:44.692754 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:08:44.798729 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:08:57.271374 WARNING::Fitting problem for feature 50 returning NA
2025-11-22 01:08:57.35053 WARNING::Fitting problem for feature 62 returning NA
2025-11-22 01:08:57.42813 WARNING::Fitting problem for feature 74 returning NA
2025-11-22 01:08:57.452232 WARNING::Fitting problem for feature 78 returning NA
2025-11-22 01:08:57.489284 WARNING::Fitting problem for feature 84 returning NA
2025-11-22 01:08:57.56896 WARNING::Fitting problem for feature 96 returning NA
2025-11-22 01:08:57.574465 WARNING::Fitting problem for feature 97 returning NA
2025-11-22 01:08:57.586537 WARNING::Fitting problem for feature 99 returning NA
2025-11-22 01:08:57.685277 WARNING::Fitting problem for feature 114 returning NA
2025-11-22 01:08:57.691463 WARNING::Fitting problem for feature 115 returning NA
2025-11-22 01:08:57.74296 WARNING::Fitting problem for feature 123 returning NA
2025-11-22 01:08:57.783926 WARNING::Fitting problem for feature 130 returning NA
2025-11-22 01:08:57.796014 WARNING::Fitting problem for feature 132 returning NA
2025-11-22 01:08:57.836924 WARNING::Fitting problem for feature 139 returning NA
2025-11-22 01:08:57.909056 WARNING::Fitting problem for feature 150 returning NA
2025-11-22 01:08:58.172866 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_linear.rds
2025-11-22 01:08:58.234134 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_linear.rds
2025-11-22 01:08:58.296721 WARNING::Deleting existing residuals file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/residuals_logistic.rds
2025-11-22 01:08:58.595768 WARNING::Deleting existing fitted file: /tmp/Rtmpt6VaQJ/file115a4e106fb4b1/fits/fitted_logistic.rds
2025-11-22 01:09:19.185843 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-22 01:09:19.203189 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-22 01:09:19.214936 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-22 01:09:19.26913 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-22 01:09:19.28596 ERROR::Effect name not found in metadata: d
2025-11-22 01:09:19.297419 ERROR::No user formula provided
2025-11-22 01:09:19.329802 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-22 01:09:19.342167 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-22 01:09:23.569654 INFO::Writing function arguments to log file
2025-11-22 01:09:23.584503 INFO::Verifying options selected are valid
2025-11-22 01:09:25.976495 INFO::Writing function arguments to log file
2025-11-22 01:09:25.988822 INFO::Verifying options selected are valid
2025-11-22 01:09:25.989972 INFO::Determining format of input files
2025-11-22 01:09:25.99101 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-22 01:09:25.993446 INFO::Running selected normalization method: TSS
2025-11-22 01:09:25.995022 INFO::Creating output feature tables folder
2025-11-22 01:09:25.996023 INFO::Writing normalized data to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/features/data_norm.tsv
2025-11-22 01:09:25.997549 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-22 01:09:25.998469 INFO::Total samples in data: 16
2025-11-22 01:09:25.999366 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-22 01:09:26.00027 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-22 01:09:26.002336 INFO::Total filtered features: 0
2025-11-22 01:09:26.003345 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-22 01:09:26.004591 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-22 01:09:26.005576 INFO::Filtered feature names from variance filtering:
2025-11-22 01:09:26.006494 INFO::Writing filtered data to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/features/filtered_data.tsv
2025-11-22 01:09:26.008034 INFO::Running selected transform method: LOG
2025-11-22 01:09:26.009269 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/features/data_transformed.tsv
2025-11-22 01:09:26.010982 INFO::Applying z-score to standardize continuous metadata
2025-11-22 01:09:26.016563 INFO::Running the linear model component
2025-11-22 01:09:26.030682 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:26.035583 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:26.040204 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:26.04797 INFO::Counting total values for each feature
2025-11-22 01:09:26.050131 INFO::Running the logistic model component
2025-11-22 01:09:26.064414 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:26.071355 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:26.077878 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:26.087304 INFO::Counting total values for each feature
2025-11-22 01:09:26.089688 INFO::Re-running abundances for warn_prevalence
2025-11-22 01:09:26.090733 INFO::Running selected normalization method: TSS
2025-11-22 01:09:26.092405 INFO::Running selected transform method: LOG
2025-11-22 01:09:26.106595 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:26.111494 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:26.116095 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:26.226526 INFO::Creating fits folder
2025-11-22 01:09:26.22783 INFO::Writing residuals to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/fits/residuals_linear.rds
2025-11-22 01:09:26.229035 INFO::Writing fitted values to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/fits/fitted_linear.rds
2025-11-22 01:09:26.230362 INFO::Writing residuals to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/fits/residuals_logistic.rds
2025-11-22 01:09:26.231662 INFO::Writing fitted values to file /tmp/Rtmpt6VaQJ/file115a4e3ca59939/fits/fitted_logistic.rds
2025-11-22 01:09:26.234551 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpt6VaQJ/file115a4e3ca59939/all_results.tsv
2025-11-22 01:09:26.236399 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/Rtmpt6VaQJ/file115a4e3ca59939/significant_results.tsv
2025-11-22 01:09:26.23788 INFO::Creating output figures folder
2025-11-22 01:09:26.239324 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpt6VaQJ/file115a4e3ca59939/figures/summary_plot.pdf
2025-11-22 01:09:27.860139 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpt6VaQJ/file115a4e3ca59939/figures
2025-11-22 01:09:27.862288 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-22 01:09:27.8675 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-22 01:09:28.436407 INFO::Writing summary plot of
significant results to file: /tmp/Rtmpt6VaQJ/file115a4e3ca59939/figures/summary_plot.pdf
2025-11-22 01:09:30.088696 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpt6VaQJ/file115a4e3ca59939/figures
2025-11-22 01:09:30.090471 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-22 01:09:30.095939 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-22 01:09:30.637036 INFO::Running the linear model component
2025-11-22 01:09:30.645943 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:30.650376 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:30.654442 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:30.661555 INFO::Counting total values for each feature
2025-11-22 01:09:30.663314 INFO::Running the logistic model component
2025-11-22 01:09:30.682146 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:30.68897 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:30.694709 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:30.703241 INFO::Counting total values for each feature
2025-11-22 01:09:30.705321 INFO::Re-running abundances for warn_prevalence
2025-11-22 01:09:30.706134 INFO::Running selected normalization method: TSS
2025-11-22 01:09:30.7075 INFO::Running selected transform method: LOG
2025-11-22 01:09:30.716051 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:30.720234 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:30.724182 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:30.818602 INFO::Creating output folder
2025-11-22 01:09:30.819613 INFO::Creating output figures folder
2025-11-22 01:09:30.820939 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpt6VaQJ/file115a4e4cbe4a5e/figures/summary_plot.pdf
2025-11-22 01:09:32.514937 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpt6VaQJ/file115a4e4cbe4a5e/figures
2025-11-22 01:09:32.517437 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-22 01:09:32.523609 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-22 01:09:33.5863 INFO::Applying z-score to standardize continuous metadata
2025-11-22 01:09:33.59491 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-22 01:09:33.595868 INFO::Bypass z-score application to metadata
2025-11-22 01:09:33.598625 INFO::Bypass z-score application to metadata
2025-11-22 01:09:33.619585 INFO::Determining format of input files
2025-11-22 01:09:33.6207 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-22 01:09:33.621639 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-22 01:09:33.6295 INFO::Determining format of input files
2025-11-22 01:09:33.630669 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-22 01:09:33.632006 INFO::Input format is feature_specific_covariate samples as columns
2025-11-22 01:09:33.648856 INFO::Determining format of input files
2025-11-22 01:09:33.650075 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-22 01:09:33.651286 INFO::Input format is feature_specific_covariate samples as columns
2025-11-22 01:09:33.653099 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-22 01:09:33.653951 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-22 01:09:33.666765 INFO::Running selected transform method: LOG
2025-11-22 01:09:33.66799 INFO::Creating output feature tables folder
2025-11-22 01:09:33.668916 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpt6VaQJ/file115a4e451125d6/features/data_transformed.tsv
2025-11-22 01:09:33.673113 INFO::Running selected transform method: LOG
2025-11-22 01:09:33.674278 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpt6VaQJ/file115a4e451125d6/features/data_transformed.tsv
2025-11-22 01:09:33.678392 INFO::Running selected transform method: PLOG
2025-11-22 01:09:33.679965 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpt6VaQJ/file115a4e451125d6/features/data_transformed.tsv
2025-11-22 01:09:33.683025 INFO::Running selected transform method: NONE
2025-11-22 01:09:33.683809 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpt6VaQJ/file115a4e451125d6/features/data_transformed.tsv
2025-11-22 01:09:33.692136 INFO::Running the linear model component
2025-11-22 01:09:33.701525 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:33.70614 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:33.710468 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:33.718117 INFO::Counting total values for each feature
2025-11-22 01:09:33.719992 INFO::Running the logistic model component
2025-11-22 01:09:33.729238 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:33.736258 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:33.742639 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:33.752104 INFO::Counting total values for each feature
2025-11-22 01:09:33.754486 INFO::Re-running abundances for warn_prevalence
2025-11-22 01:09:33.755478 INFO::Running selected normalization method: TSS
2025-11-22 01:09:33.757036 INFO::Running selected transform method: LOG
2025-11-22 01:09:33.766392 INFO::Fitting model to feature number 1, a
2025-11-22 01:09:33.77067 INFO::Fitting model to feature number 2, b
2025-11-22 01:09:33.774793 INFO::Fitting model to feature number 3, c
2025-11-22 01:09:33.866293 INFO::Creating output folder
2025-11-22 01:09:33.867349 INFO::Creating fits folder
2025-11-22 01:09:33.868265 INFO::Writing residuals to file /tmp/Rtmpt6VaQJ/file115a4e64f838d7/fits/residuals_linear.rds
2025-11-22 01:09:33.869284 INFO::Writing fitted values to file /tmp/Rtmpt6VaQJ/file115a4e64f838d7/fits/fitted_linear.rds
2025-11-22 01:09:33.870492 INFO::Writing residuals to file /tmp/Rtmpt6VaQJ/file115a4e64f838d7/fits/residuals_logistic.rds
2025-11-22 01:09:33.871629 INFO::Writing fitted values to file /tmp/Rtmpt6VaQJ/file115a4e64f838d7/fits/fitted_logistic.rds
2025-11-22 01:09:33.874305 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpt6VaQJ/file115a4e64f838d7/all_results.tsv
2025-11-22 01:09:33.875864 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/Rtmpt6VaQJ/file115a4e64f838d7/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
362.741 4.817 367.556
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 20.150 | 0.553 | 20.707 | |
| maaslin_check_arguments | 0.136 | 0.002 | 0.138 | |
| maaslin_check_formula | 0.135 | 0.001 | 0.136 | |
| maaslin_compute_formula | 0.153 | 0.007 | 0.160 | |
| maaslin_contrast_test | 18.202 | 0.448 | 18.658 | |
| maaslin_filter | 0.475 | 0.017 | 0.492 | |
| maaslin_fit | 12.602 | 0.081 | 12.683 | |
| maaslin_log_arguments | 0.133 | 0.000 | 0.132 | |
| maaslin_normalize | 0.266 | 0.006 | 0.272 | |
| maaslin_plot_results | 42.633 | 0.445 | 43.039 | |
| maaslin_plot_results_from_output | 42.567 | 0.348 | 42.924 | |
| maaslin_process_metadata | 0.480 | 0.024 | 0.503 | |
| maaslin_read_data | 0.138 | 0.004 | 0.141 | |
| maaslin_reorder_data | 0.151 | 0.004 | 0.156 | |
| maaslin_transform | 0.537 | 0.027 | 0.565 | |
| maaslin_write_results | 13.709 | 0.222 | 13.932 | |
| maaslin_write_results_lefse_format | 14.184 | 0.127 | 14.313 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.005 | 0.000 | 0.004 | |