William Nickols
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:01 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.2.0.tar.gz |
| StartedAt: 2025-12-02 07:20:52 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 07:49:02 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 1689.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 102.035 1.536 108.535
maaslin_plot_results_from_output 101.135 1.260 106.506
maaslin_contrast_test 42.427 1.938 46.466
maaslin3 40.939 1.554 46.037
maaslin_write_results_lefse_format 37.288 0.715 45.298
maaslin_write_results 32.754 0.978 35.648
maaslin_fit 30.628 1.074 34.109
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
maaslin3.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maaslin3)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
2025-12-02 07:34:59.790947 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:35:00.740398 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:35:00.97544 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:35:01.036764 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:35:01.140347 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:35:01.386771 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:35:01.401112 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:35:01.434183 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:35:01.706431 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:35:01.72147 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:35:01.871011 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:35:01.988203 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:35:02.038688 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:35:02.147458 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:35:02.348491 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:35:36.409246 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:35:36.621991 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:35:36.834296 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:35:36.894444 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:35:36.985964 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:35:37.197189 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:35:37.210953 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:35:37.24345 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:35:37.517175 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:35:37.53268 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:35:37.676519 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:35:37.81675 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:35:37.850361 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:35:37.967417 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:35:38.164195 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:35:47.810 R[31825:80625563] XType: com.apple.fonts is not accessible.
2025-12-02 07:35:47.810 R[31825:80625563] XType: XTFontStaticRegistry is enabled.
2025-12-02 07:36:36.219782 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:36:36.438662 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:36:36.656638 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:36:36.718969 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:36:36.816967 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:36:37.02628 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:36:37.040815 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:36:37.07475 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:36:37.330657 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:36:37.345106 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:36:37.491196 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:36:37.608207 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:36:37.642741 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:36:37.766135 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:36:37.990094 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:37:08.592667 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:37:08.821886 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:37:09.049754 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:37:09.113029 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:37:09.2082 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:37:09.423595 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:37:09.438242 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:37:09.47203 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:37:09.753525 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:37:09.768811 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:37:09.923058 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:37:10.052437 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:37:10.086317 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:37:10.217871 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:37:10.476021 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:37:11.031099 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/residuals_linear.rds
2025-12-02 07:37:11.153696 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/fitted_linear.rds
2025-12-02 07:37:11.264346 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/residuals_logistic.rds
2025-12-02 07:37:11.848171 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/fitted_logistic.rds
2025-12-02 07:38:00.975516 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:38:01.187397 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:38:01.401502 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:38:01.462535 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:38:01.557154 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:38:01.755547 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:38:01.768729 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:38:01.799195 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:38:02.061286 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:38:02.077577 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:38:02.212715 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:38:02.322944 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:38:02.355148 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:38:02.46982 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:38:02.705329 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:38:32.830091 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:38:33.051748 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:38:33.259199 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:38:33.319549 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:38:33.414437 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:38:33.611939 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:38:33.65004 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:38:33.680392 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:38:33.935003 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:38:33.949463 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:38:34.084272 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:38:34.191499 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:38:34.224484 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:38:34.331592 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:38:34.535275 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:38:35.065194 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/residuals_linear.rds
2025-12-02 07:38:35.178311 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/fitted_linear.rds
2025-12-02 07:38:35.286082 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/residuals_logistic.rds
2025-12-02 07:38:35.855621 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/fitted_logistic.rds
2025-12-02 07:39:24.676536 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:39:24.878006 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:39:25.081167 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:39:25.141295 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:39:25.236352 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:39:25.452988 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:39:25.466876 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:39:25.4989 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:39:25.777587 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:39:25.79476 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:39:25.950059 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:39:26.075625 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:39:26.111952 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:39:26.230575 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:39:26.442151 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:39:56.652091 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:39:56.858825 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:39:57.056698 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:39:57.119147 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:39:57.218649 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:39:57.422053 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:39:57.436087 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:39:57.467741 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:39:57.724528 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:39:57.740276 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:39:57.869854 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:39:57.977448 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:39:58.008764 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:39:58.115416 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:39:58.302535 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:39:58.824818 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/residuals_linear.rds
2025-12-02 07:39:58.930139 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/fitted_linear.rds
2025-12-02 07:39:59.05697 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/residuals_logistic.rds
2025-12-02 07:39:59.642107 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c5177e3df19/fits/fitted_logistic.rds
2025-12-02 07:40:47.771385 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:40:47.98688 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:40:48.189872 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:40:48.249501 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:40:48.339128 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:40:48.548597 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:40:48.571099 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:40:48.605871 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:40:48.908395 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:40:48.92472 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:40:49.05763 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:40:49.156325 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:40:49.187911 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:40:49.299958 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:40:49.488144 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:41:16.69799 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:41:16.894426 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:41:17.097277 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:41:17.156636 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:41:17.249617 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:41:17.453004 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:41:17.46707 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:41:17.49866 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:41:17.754329 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:41:17.768811 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:41:17.896951 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:41:18.00325 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:41:18.033658 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:41:18.140048 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:41:18.329856 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:42:12.294926 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:42:34.956896 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:43:31.71745 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:43:50.491762 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:43:52.173779 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_linear.rds
2025-12-02 07:43:52.280813 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_linear.rds
2025-12-02 07:43:52.343931 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_logistic.rds
2025-12-02 07:43:52.479569 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_logistic.rds
2025-12-02 07:44:45.272621 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:44:57.928165 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:44:58.73019 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_linear.rds
2025-12-02 07:44:58.844613 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_linear.rds
2025-12-02 07:44:58.916145 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_logistic.rds
2025-12-02 07:44:59.057033 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_logistic.rds
2025-12-02 07:45:43.74001 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:45:56.910986 WARNING::Fitting problem for feature 124 returning NA
2025-12-02 07:45:57.773005 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_linear.rds
2025-12-02 07:45:57.880335 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_linear.rds
2025-12-02 07:45:57.953778 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_logistic.rds
2025-12-02 07:45:58.094641 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_logistic.rds
2025-12-02 07:46:42.256968 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:46:42.478924 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:46:42.725085 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:46:42.793235 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:46:42.896328 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:46:43.111294 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:46:43.127907 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:46:43.161721 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:46:43.443594 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:46:43.457986 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:46:43.607618 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:46:43.725004 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:46:43.760033 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:46:43.886292 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:46:44.131414 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:47:15.052142 WARNING::Fitting problem for feature 50 returning NA
2025-12-02 07:47:15.27166 WARNING::Fitting problem for feature 62 returning NA
2025-12-02 07:47:15.48874 WARNING::Fitting problem for feature 74 returning NA
2025-12-02 07:47:15.553209 WARNING::Fitting problem for feature 78 returning NA
2025-12-02 07:47:15.658081 WARNING::Fitting problem for feature 84 returning NA
2025-12-02 07:47:15.889477 WARNING::Fitting problem for feature 96 returning NA
2025-12-02 07:47:15.906185 WARNING::Fitting problem for feature 97 returning NA
2025-12-02 07:47:15.940558 WARNING::Fitting problem for feature 99 returning NA
2025-12-02 07:47:16.221962 WARNING::Fitting problem for feature 114 returning NA
2025-12-02 07:47:16.23704 WARNING::Fitting problem for feature 115 returning NA
2025-12-02 07:47:16.382507 WARNING::Fitting problem for feature 123 returning NA
2025-12-02 07:47:16.504419 WARNING::Fitting problem for feature 130 returning NA
2025-12-02 07:47:16.537512 WARNING::Fitting problem for feature 132 returning NA
2025-12-02 07:47:16.654777 WARNING::Fitting problem for feature 139 returning NA
2025-12-02 07:47:16.860069 WARNING::Fitting problem for feature 150 returning NA
2025-12-02 07:47:17.580849 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_linear.rds
2025-12-02 07:47:17.691715 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_linear.rds
2025-12-02 07:47:17.829084 WARNING::Deleting existing residuals file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/residuals_logistic.rds
2025-12-02 07:47:18.435742 WARNING::Deleting existing fitted file: /tmp/RtmpxxiqtR/file7c51524fe3f/fits/fitted_logistic.rds
2025-12-02 07:48:10.763698 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-02 07:48:10.809135 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-02 07:48:10.841112 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-02 07:48:10.983755 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-02 07:48:11.030354 ERROR::Effect name not found in metadata: d
2025-12-02 07:48:11.061369 ERROR::No user formula provided
2025-12-02 07:48:11.150219 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-02 07:48:11.184677 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-02 07:48:20.828695 INFO::Writing function arguments to log file
2025-12-02 07:48:20.874747 INFO::Verifying options selected are valid
2025-12-02 07:48:26.703236 INFO::Writing function arguments to log file
2025-12-02 07:48:26.741895 INFO::Verifying options selected are valid
2025-12-02 07:48:26.744734 INFO::Determining format of input files
2025-12-02 07:48:26.747734 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 07:48:26.754154 INFO::Running selected normalization method: TSS
2025-12-02 07:48:26.757969 INFO::Creating output feature tables folder
2025-12-02 07:48:26.761024 INFO::Writing normalized data to file /tmp/RtmpxxiqtR/file7c5126a7bc70/features/data_norm.tsv
2025-12-02 07:48:26.765376 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-02 07:48:26.772125 INFO::Total samples in data: 16
2025-12-02 07:48:26.775519 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-02 07:48:26.77833 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-02 07:48:26.784112 INFO::Total filtered features: 0
2025-12-02 07:48:26.786962 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-02 07:48:26.790123 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-02 07:48:26.793192 INFO::Filtered feature names from variance filtering:
2025-12-02 07:48:26.795896 INFO::Writing filtered data to file /tmp/RtmpxxiqtR/file7c5126a7bc70/features/filtered_data.tsv
2025-12-02 07:48:26.801019 INFO::Running selected transform method: LOG
2025-12-02 07:48:26.804477 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpxxiqtR/file7c5126a7bc70/features/data_transformed.tsv
2025-12-02 07:48:26.809827 INFO::Applying z-score to standardize continuous metadata
2025-12-02 07:48:26.822027 INFO::Running the linear model component
2025-12-02 07:48:26.865615 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:26.87751 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:26.888585 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:26.907346 INFO::Counting total values for each feature
2025-12-02 07:48:26.912492 INFO::Running the logistic model component
2025-12-02 07:48:26.952874 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:26.96915 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:26.98414 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:27.006969 INFO::Counting total values for each feature
2025-12-02 07:48:27.012648 INFO::Re-running abundances for warn_prevalence
2025-12-02 07:48:27.016431 INFO::Running selected normalization method: TSS
2025-12-02 07:48:27.020736 INFO::Running selected transform method: LOG
2025-12-02 07:48:27.199425 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:27.211216 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:27.22356 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:27.452605 INFO::Creating fits folder
2025-12-02 07:48:27.455839 INFO::Writing residuals to file /tmp/RtmpxxiqtR/file7c5126a7bc70/fits/residuals_linear.rds
2025-12-02 07:48:27.459404 INFO::Writing fitted values to file /tmp/RtmpxxiqtR/file7c5126a7bc70/fits/fitted_linear.rds
2025-12-02 07:48:27.462927 INFO::Writing residuals to file /tmp/RtmpxxiqtR/file7c5126a7bc70/fits/residuals_logistic.rds
2025-12-02 07:48:27.466206 INFO::Writing fitted values to file /tmp/RtmpxxiqtR/file7c5126a7bc70/fits/fitted_logistic.rds
2025-12-02 07:48:27.472899 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpxxiqtR/file7c5126a7bc70/all_results.tsv
2025-12-02 07:48:27.477595 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/RtmpxxiqtR/file7c5126a7bc70/significant_results.tsv
2025-12-02 07:48:27.481464 INFO::Creating output figures folder
2025-12-02 07:48:27.485649 INFO::Writing summary plot of significant
results to file: /tmp/RtmpxxiqtR/file7c5126a7bc70/figures/summary_plot.pdf
2025-12-02 07:48:31.403393 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpxxiqtR/file7c5126a7bc70/figures
2025-12-02 07:48:31.408123 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 07:48:31.421827 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 07:48:32.814789 INFO::Writing summary plot of
significant results to file: /tmp/RtmpxxiqtR/file7c5126a7bc70/figures/summary_plot.pdf
2025-12-02 07:48:36.743831 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpxxiqtR/file7c5126a7bc70/figures
2025-12-02 07:48:36.748445 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 07:48:36.763956 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 07:48:38.121134 INFO::Running the linear model component
2025-12-02 07:48:38.143951 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:38.155247 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:38.166527 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:38.184978 INFO::Counting total values for each feature
2025-12-02 07:48:38.189262 INFO::Running the logistic model component
2025-12-02 07:48:38.212079 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:38.229119 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:38.245208 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:38.267953 INFO::Counting total values for each feature
2025-12-02 07:48:38.272759 INFO::Re-running abundances for warn_prevalence
2025-12-02 07:48:38.27498 INFO::Running selected normalization method: TSS
2025-12-02 07:48:38.27881 INFO::Running selected transform method: LOG
2025-12-02 07:48:38.304212 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:38.318018 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:38.328422 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:38.561241 INFO::Creating output folder
2025-12-02 07:48:38.563544 INFO::Creating output figures folder
2025-12-02 07:48:38.566917 INFO::Writing summary plot of significant
results to file: /tmp/RtmpxxiqtR/file7c51480f4046/figures/summary_plot.pdf
2025-12-02 07:48:42.68466 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpxxiqtR/file7c51480f4046/figures
2025-12-02 07:48:42.688115 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-02 07:48:42.699585 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-02 07:48:45.182672 INFO::Applying z-score to standardize continuous metadata
2025-12-02 07:48:45.200134 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-02 07:48:45.202208 INFO::Bypass z-score application to metadata
2025-12-02 07:48:45.208545 INFO::Bypass z-score application to metadata
2025-12-02 07:48:45.256889 INFO::Determining format of input files
2025-12-02 07:48:45.258943 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 07:48:45.260994 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-02 07:48:45.280385 INFO::Determining format of input files
2025-12-02 07:48:45.28288 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-02 07:48:45.286335 INFO::Input format is feature_specific_covariate samples as columns
2025-12-02 07:48:45.306752 INFO::Determining format of input files
2025-12-02 07:48:45.30907 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-02 07:48:45.311629 INFO::Input format is feature_specific_covariate samples as columns
2025-12-02 07:48:45.315881 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-02 07:48:45.317852 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-02 07:48:45.345336 INFO::Running selected transform method: LOG
2025-12-02 07:48:45.347916 INFO::Creating output feature tables folder
2025-12-02 07:48:45.350395 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpxxiqtR/file7c513c995aa7/features/data_transformed.tsv
2025-12-02 07:48:45.360563 INFO::Running selected transform method: LOG
2025-12-02 07:48:45.363365 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpxxiqtR/file7c513c995aa7/features/data_transformed.tsv
2025-12-02 07:48:45.372994 INFO::Running selected transform method: PLOG
2025-12-02 07:48:45.377158 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpxxiqtR/file7c513c995aa7/features/data_transformed.tsv
2025-12-02 07:48:45.384812 INFO::Running selected transform method: NONE
2025-12-02 07:48:45.38667 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpxxiqtR/file7c513c995aa7/features/data_transformed.tsv
2025-12-02 07:48:45.404953 INFO::Running the linear model component
2025-12-02 07:48:45.427605 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:45.438224 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:45.448622 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:45.465508 INFO::Counting total values for each feature
2025-12-02 07:48:45.469719 INFO::Running the logistic model component
2025-12-02 07:48:45.491361 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:45.506484 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:45.521661 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:45.544563 INFO::Counting total values for each feature
2025-12-02 07:48:45.549667 INFO::Re-running abundances for warn_prevalence
2025-12-02 07:48:45.551705 INFO::Running selected normalization method: TSS
2025-12-02 07:48:45.555162 INFO::Running selected transform method: LOG
2025-12-02 07:48:45.577106 INFO::Fitting model to feature number 1, a
2025-12-02 07:48:45.586028 INFO::Fitting model to feature number 2, b
2025-12-02 07:48:45.595859 INFO::Fitting model to feature number 3, c
2025-12-02 07:48:45.804931 INFO::Creating output folder
2025-12-02 07:48:45.807269 INFO::Creating fits folder
2025-12-02 07:48:45.809406 INFO::Writing residuals to file /tmp/RtmpxxiqtR/file7c51780ea905/fits/residuals_linear.rds
2025-12-02 07:48:45.812167 INFO::Writing fitted values to file /tmp/RtmpxxiqtR/file7c51780ea905/fits/fitted_linear.rds
2025-12-02 07:48:45.815232 INFO::Writing residuals to file /tmp/RtmpxxiqtR/file7c51780ea905/fits/residuals_logistic.rds
2025-12-02 07:48:45.818268 INFO::Writing fitted values to file /tmp/RtmpxxiqtR/file7c51780ea905/fits/fitted_logistic.rds
2025-12-02 07:48:45.824998 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpxxiqtR/file7c51780ea905/all_results.tsv
2025-12-02 07:48:45.829411 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/RtmpxxiqtR/file7c51780ea905/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
805.256 12.850 849.779
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 40.939 | 1.554 | 46.037 | |
| maaslin_check_arguments | 0.283 | 0.007 | 0.303 | |
| maaslin_check_formula | 0.302 | 0.015 | 0.372 | |
| maaslin_compute_formula | 0.354 | 0.017 | 0.382 | |
| maaslin_contrast_test | 42.427 | 1.938 | 46.466 | |
| maaslin_filter | 1.216 | 0.075 | 1.313 | |
| maaslin_fit | 30.628 | 1.074 | 34.109 | |
| maaslin_log_arguments | 0.293 | 0.014 | 0.325 | |
| maaslin_normalize | 0.697 | 0.045 | 0.785 | |
| maaslin_plot_results | 102.035 | 1.536 | 108.535 | |
| maaslin_plot_results_from_output | 101.135 | 1.260 | 106.506 | |
| maaslin_process_metadata | 1.225 | 0.077 | 1.428 | |
| maaslin_read_data | 0.284 | 0.014 | 0.328 | |
| maaslin_reorder_data | 0.305 | 0.016 | 0.346 | |
| maaslin_transform | 1.568 | 0.111 | 1.859 | |
| maaslin_write_results | 32.754 | 0.978 | 35.648 | |
| maaslin_write_results_lefse_format | 37.288 | 0.715 | 45.298 | |
| preprocess_dna_mtx | 0.009 | 0.001 | 0.010 | |
| preprocess_taxa_mtx | 0.010 | 0.001 | 0.012 | |