William Nickols
| Snapshot Date: 2025-12-15 13:40 -0500 (Mon, 15 Dec 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 2025-12-16 11:34 -0500 (Tue, 16 Dec 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" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 1158/2332 | 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 | | ||||||||
| 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: 2025-12-16 00:33:07 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 00:54:46 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 1299.8 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 43.723 0.249 43.939
maaslin_plot_results_from_output 43.106 0.393 43.503
maaslin3 19.017 0.574 19.594
maaslin_contrast_test 18.807 0.448 19.257
maaslin_write_results_lefse_format 14.724 0.055 14.783
maaslin_write_results 13.759 0.154 13.914
maaslin_fit 12.439 0.171 12.610
* 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")
2025-12-16 00:39:21.958137 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:39:22.036851 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:39:22.132987 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:39:22.159613 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:39:22.207597 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:39:22.284381 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:39:22.289921 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:39:22.301866 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:39:22.411497 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:39:22.417296 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:39:22.471184 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:39:22.512875 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:39:22.524684 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:39:22.564734 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:39:22.641152 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:39:38.874989 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:39:38.951614 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:39:39.026886 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:39:39.050951 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:39:39.085539 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:39:39.187866 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:39:39.193412 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:39:39.205667 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:39:39.30039 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:39:39.305851 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:39:39.3562 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:39:39.397042 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:39:39.408771 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:39:39.448094 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:39:39.516874 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:40:03.72368 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:40:03.80251 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:40:03.877236 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:40:03.899071 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:40:03.933366 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:40:04.008047 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:40:04.013381 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:40:04.025101 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:40:04.129846 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:40:04.135921 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:40:04.188532 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:40:04.232025 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:40:04.245512 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:40:04.2905 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:40:04.363098 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:40:17.334428 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:40:17.411306 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:40:17.487464 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:40:17.509317 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:40:17.543904 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:40:17.62038 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:40:17.626038 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:40:17.638238 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:40:17.736948 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:40:17.742692 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:40:17.795648 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:40:17.837757 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:40:17.850618 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:40:17.891855 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:40:17.984308 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:40:18.183877 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/residuals_linear.rds
2025-12-16 00:40:18.2449 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/fitted_linear.rds
2025-12-16 00:40:18.30779 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/residuals_logistic.rds
2025-12-16 00:40:18.607149 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/fitted_logistic.rds
2025-12-16 00:40:39.962992 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:40:40.041016 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:40:40.118094 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:40:40.139847 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:40:40.174483 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:40:40.252483 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:40:40.25826 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:40:40.271356 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:40:40.375865 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:40:40.382922 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:40:40.438879 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:40:40.483479 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:40:40.495861 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:40:40.537639 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:40:40.610193 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:40:53.463121 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:40:53.537968 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:40:53.611866 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:40:53.633837 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:40:53.667505 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:40:53.742754 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:40:53.748823 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:40:53.761622 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:40:53.858873 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:40:53.864813 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:40:53.945235 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:40:53.986764 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:40:53.999028 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:40:54.040415 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:40:54.11061 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:40:54.319398 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/residuals_linear.rds
2025-12-16 00:40:54.380225 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/fitted_linear.rds
2025-12-16 00:40:54.443098 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/residuals_logistic.rds
2025-12-16 00:40:54.742301 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/fitted_logistic.rds
2025-12-16 00:41:16.727459 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:41:16.808036 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:41:16.888348 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:41:16.911401 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:41:16.945895 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:41:17.020775 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:41:17.026092 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:41:17.038307 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:41:17.133751 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:41:17.139244 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:41:17.188713 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:41:17.229343 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:41:17.241336 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:41:17.28157 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:41:17.352238 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:41:28.260127 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:41:28.337395 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:41:28.414445 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:41:28.437246 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:41:28.472675 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:41:28.550793 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:41:28.556405 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:41:28.568936 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:41:28.667176 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:41:28.672995 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:41:28.72503 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:41:28.765534 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:41:28.777509 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:41:28.818777 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:41:28.890956 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:41:29.129805 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/residuals_linear.rds
2025-12-16 00:41:29.190448 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/fitted_linear.rds
2025-12-16 00:41:29.253224 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/residuals_logistic.rds
2025-12-16 00:41:29.552936 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb1ad876bb/fits/fitted_logistic.rds
2025-12-16 00:41:50.582298 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:41:50.659916 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:41:50.736973 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:41:50.759407 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:41:50.794667 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:41:50.899446 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:41:50.905343 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:41:50.918233 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:41:51.016212 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:41:51.02176 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:41:51.072096 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:41:51.113213 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:41:51.12585 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:41:51.16799 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:41:51.237063 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:42:03.255023 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:42:03.33608 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:42:03.417632 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:42:03.440997 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:42:03.476344 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:42:03.553556 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:42:03.55919 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:42:03.57107 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:42:03.667407 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:42:03.672909 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:42:03.72299 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:42:03.763355 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:42:03.775291 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:42:03.816702 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:42:03.890065 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:42:27.373812 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:42:36.208205 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:43:02.822107 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:43:11.37716 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:43:12.038628 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_linear.rds
2025-12-16 00:43:12.100231 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_linear.rds
2025-12-16 00:43:12.139132 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_logistic.rds
2025-12-16 00:43:12.208211 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_logistic.rds
2025-12-16 00:43:35.338808 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:43:42.178474 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:43:42.52841 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_linear.rds
2025-12-16 00:43:42.590086 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_linear.rds
2025-12-16 00:43:42.62853 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_logistic.rds
2025-12-16 00:43:42.697525 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_logistic.rds
2025-12-16 00:44:01.325539 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:44:07.789168 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 00:44:08.085311 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_linear.rds
2025-12-16 00:44:08.146628 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_linear.rds
2025-12-16 00:44:08.185169 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_logistic.rds
2025-12-16 00:44:08.254109 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_logistic.rds
2025-12-16 00:44:26.009 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:44:26.085848 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:44:26.160327 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:44:26.182678 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:44:26.227992 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:44:26.305151 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:44:26.310593 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:44:26.322544 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:44:26.423125 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:44:26.42941 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:44:26.483209 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:44:26.52528 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:44:26.538105 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:44:26.58015 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:44:26.650531 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:44:38.484254 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 00:44:38.558353 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 00:44:38.667423 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 00:44:38.691165 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 00:44:38.726178 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 00:44:38.803168 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 00:44:38.808623 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 00:44:38.820583 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 00:44:38.916955 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 00:44:38.922363 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 00:44:38.971774 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 00:44:39.012202 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 00:44:39.024012 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 00:44:39.064272 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 00:44:39.132581 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 00:44:39.383136 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_linear.rds
2025-12-16 00:44:39.444048 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_linear.rds
2025-12-16 00:44:39.506974 WARNING::Deleting existing residuals file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/residuals_logistic.rds
2025-12-16 00:44:39.806221 WARNING::Deleting existing fitted file: /tmp/Rtmpmcvrtk/file34cedb3e96870c/fits/fitted_logistic.rds
2025-12-16 00:44:59.827331 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-16 00:44:59.844114 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-16 00:44:59.855709 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-16 00:44:59.918214 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-16 00:44:59.934515 ERROR::Effect name not found in metadata: d
2025-12-16 00:44:59.945661 ERROR::No user formula provided
2025-12-16 00:44:59.977375 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-16 00:44:59.989197 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-16 00:45:02.893547 INFO::Writing function arguments to log file
2025-12-16 00:45:02.907639 INFO::Verifying options selected are valid
2025-12-16 00:45:05.340971 INFO::Writing function arguments to log file
2025-12-16 00:45:05.353412 INFO::Verifying options selected are valid
2025-12-16 00:45:05.354606 INFO::Determining format of input files
2025-12-16 00:45:05.355641 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 00:45:05.358073 INFO::Running selected normalization method: TSS
2025-12-16 00:45:05.359592 INFO::Creating output feature tables folder
2025-12-16 00:45:05.3606 INFO::Writing normalized data to file /tmp/Rtmpmcvrtk/file34cedb51c67779/features/data_norm.tsv
2025-12-16 00:45:05.36214 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-16 00:45:05.363065 INFO::Total samples in data: 16
2025-12-16 00:45:05.363958 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-16 00:45:05.364846 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-16 00:45:05.366846 INFO::Total filtered features: 0
2025-12-16 00:45:05.367827 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-16 00:45:05.369039 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-16 00:45:05.369991 INFO::Filtered feature names from variance filtering:
2025-12-16 00:45:05.370884 INFO::Writing filtered data to file /tmp/Rtmpmcvrtk/file34cedb51c67779/features/filtered_data.tsv
2025-12-16 00:45:05.372401 INFO::Running selected transform method: LOG
2025-12-16 00:45:05.373641 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpmcvrtk/file34cedb51c67779/features/data_transformed.tsv
2025-12-16 00:45:05.375347 INFO::Applying z-score to standardize continuous metadata
2025-12-16 00:45:05.380731 INFO::Running the linear model component
2025-12-16 00:45:05.394715 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:05.399571 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:05.404185 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:05.411918 INFO::Counting total values for each feature
2025-12-16 00:45:05.413963 INFO::Running the logistic model component
2025-12-16 00:45:05.428247 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:05.435373 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:05.441982 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:05.451964 INFO::Counting total values for each feature
2025-12-16 00:45:05.454572 INFO::Re-running abundances for warn_prevalence
2025-12-16 00:45:05.455663 INFO::Running selected normalization method: TSS
2025-12-16 00:45:05.457351 INFO::Running selected transform method: LOG
2025-12-16 00:45:05.472489 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:05.477612 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:05.482229 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:05.574438 INFO::Creating fits folder
2025-12-16 00:45:05.575814 INFO::Writing residuals to file /tmp/Rtmpmcvrtk/file34cedb51c67779/fits/residuals_linear.rds
2025-12-16 00:45:05.577021 INFO::Writing fitted values to file /tmp/Rtmpmcvrtk/file34cedb51c67779/fits/fitted_linear.rds
2025-12-16 00:45:05.578312 INFO::Writing residuals to file /tmp/Rtmpmcvrtk/file34cedb51c67779/fits/residuals_logistic.rds
2025-12-16 00:45:05.579561 INFO::Writing fitted values to file /tmp/Rtmpmcvrtk/file34cedb51c67779/fits/fitted_logistic.rds
2025-12-16 00:45:05.582324 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpmcvrtk/file34cedb51c67779/all_results.tsv
2025-12-16 00:45:05.584014 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/Rtmpmcvrtk/file34cedb51c67779/significant_results.tsv
2025-12-16 00:45:05.585388 INFO::Creating output figures folder
2025-12-16 00:45:05.586816 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpmcvrtk/file34cedb51c67779/figures/summary_plot.pdf
2025-12-16 00:45:07.169008 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpmcvrtk/file34cedb51c67779/figures
2025-12-16 00:45:07.171084 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 00:45:07.176169 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 00:45:07.771945 INFO::Writing summary plot of
significant results to file: /tmp/Rtmpmcvrtk/file34cedb51c67779/figures/summary_plot.pdf
2025-12-16 00:45:09.523453 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpmcvrtk/file34cedb51c67779/figures
2025-12-16 00:45:09.525271 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 00:45:09.530775 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 00:45:10.065772 INFO::Running the linear model component
2025-12-16 00:45:10.076015 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:10.081319 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:10.085908 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:10.093505 INFO::Counting total values for each feature
2025-12-16 00:45:10.095217 INFO::Running the logistic model component
2025-12-16 00:45:10.103706 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:10.109748 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:10.115553 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:10.124357 INFO::Counting total values for each feature
2025-12-16 00:45:10.126396 INFO::Re-running abundances for warn_prevalence
2025-12-16 00:45:10.127161 INFO::Running selected normalization method: TSS
2025-12-16 00:45:10.128501 INFO::Running selected transform method: LOG
2025-12-16 00:45:10.1371 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:10.141091 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:10.144888 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:10.230201 INFO::Creating output folder
2025-12-16 00:45:10.231188 INFO::Creating output figures folder
2025-12-16 00:45:10.232468 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpmcvrtk/file34cedbbe57403/figures/summary_plot.pdf
2025-12-16 00:45:11.879375 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpmcvrtk/file34cedbbe57403/figures
2025-12-16 00:45:11.881613 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 00:45:11.887592 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 00:45:12.894117 INFO::Applying z-score to standardize continuous metadata
2025-12-16 00:45:12.90273 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-16 00:45:12.903702 INFO::Bypass z-score application to metadata
2025-12-16 00:45:12.906374 INFO::Bypass z-score application to metadata
2025-12-16 00:45:12.926104 INFO::Determining format of input files
2025-12-16 00:45:12.927184 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 00:45:12.92817 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-16 00:45:12.936379 INFO::Determining format of input files
2025-12-16 00:45:12.937638 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-16 00:45:12.939132 INFO::Input format is feature_specific_covariate samples as columns
2025-12-16 00:45:12.948267 INFO::Determining format of input files
2025-12-16 00:45:12.949413 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 00:45:12.950635 INFO::Input format is feature_specific_covariate samples as columns
2025-12-16 00:45:12.952438 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-16 00:45:12.953305 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-16 00:45:12.966644 INFO::Running selected transform method: LOG
2025-12-16 00:45:12.967865 INFO::Creating output feature tables folder
2025-12-16 00:45:12.968729 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpmcvrtk/file34cedb46e4e73d/features/data_transformed.tsv
2025-12-16 00:45:12.972765 INFO::Running selected transform method: LOG
2025-12-16 00:45:12.973826 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpmcvrtk/file34cedb46e4e73d/features/data_transformed.tsv
2025-12-16 00:45:12.982038 INFO::Running selected transform method: PLOG
2025-12-16 00:45:12.983708 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpmcvrtk/file34cedb46e4e73d/features/data_transformed.tsv
2025-12-16 00:45:12.98657 INFO::Running selected transform method: NONE
2025-12-16 00:45:12.987336 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpmcvrtk/file34cedb46e4e73d/features/data_transformed.tsv
2025-12-16 00:45:13.00883 INFO::Running the linear model component
2025-12-16 00:45:13.024324 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:13.031247 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:13.037858 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:13.049202 INFO::Counting total values for each feature
2025-12-16 00:45:13.052061 INFO::Running the logistic model component
2025-12-16 00:45:13.067108 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:13.077165 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:13.08629 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:13.095572 INFO::Counting total values for each feature
2025-12-16 00:45:13.097774 INFO::Re-running abundances for warn_prevalence
2025-12-16 00:45:13.098671 INFO::Running selected normalization method: TSS
2025-12-16 00:45:13.100132 INFO::Running selected transform method: LOG
2025-12-16 00:45:13.108949 INFO::Fitting model to feature number 1, a
2025-12-16 00:45:13.113229 INFO::Fitting model to feature number 2, b
2025-12-16 00:45:13.117148 INFO::Fitting model to feature number 3, c
2025-12-16 00:45:13.208848 INFO::Creating output folder
2025-12-16 00:45:13.209964 INFO::Creating fits folder
2025-12-16 00:45:13.210878 INFO::Writing residuals to file /tmp/Rtmpmcvrtk/file34cedb7dac43a0/fits/residuals_linear.rds
2025-12-16 00:45:13.211886 INFO::Writing fitted values to file /tmp/Rtmpmcvrtk/file34cedb7dac43a0/fits/fitted_linear.rds
2025-12-16 00:45:13.21297 INFO::Writing residuals to file /tmp/Rtmpmcvrtk/file34cedb7dac43a0/fits/residuals_logistic.rds
2025-12-16 00:45:13.21406 INFO::Writing fitted values to file /tmp/Rtmpmcvrtk/file34cedb7dac43a0/fits/fitted_logistic.rds
2025-12-16 00:45:13.216658 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpmcvrtk/file34cedb7dac43a0/all_results.tsv
2025-12-16 00:45:13.218204 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/Rtmpmcvrtk/file34cedb7dac43a0/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
357.190 5.292 362.563
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 19.017 | 0.574 | 19.594 | |
| maaslin_check_arguments | 0.140 | 0.007 | 0.147 | |
| maaslin_check_formula | 0.143 | 0.005 | 0.148 | |
| maaslin_compute_formula | 0.156 | 0.010 | 0.167 | |
| maaslin_contrast_test | 18.807 | 0.448 | 19.257 | |
| maaslin_filter | 0.463 | 0.010 | 0.472 | |
| maaslin_fit | 12.439 | 0.171 | 12.610 | |
| maaslin_log_arguments | 0.126 | 0.004 | 0.130 | |
| maaslin_normalize | 0.259 | 0.006 | 0.265 | |
| maaslin_plot_results | 43.723 | 0.249 | 43.939 | |
| maaslin_plot_results_from_output | 43.106 | 0.393 | 43.503 | |
| maaslin_process_metadata | 0.475 | 0.014 | 0.488 | |
| maaslin_read_data | 0.132 | 0.002 | 0.133 | |
| maaslin_reorder_data | 0.133 | 0.004 | 0.136 | |
| maaslin_transform | 0.540 | 0.014 | 0.553 | |
| maaslin_write_results | 13.759 | 0.154 | 13.914 | |
| maaslin_write_results_lefse_format | 14.724 | 0.055 | 14.783 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.003 | 0.000 | 0.005 | |