William Nickols
| Snapshot Date: 2025-11-17 13:40 -0500 (Mon, 17 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 2025-11-18 11:40 -0500 (Tue, 18 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" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4561 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 1152/2325 | 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: /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_1.3.0.tar.gz |
| StartedAt: 2025-11-17 21:40:41 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 21:46:10 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 328.5 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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_from_output 16.988 0.702 18.767
maaslin_plot_results 16.885 0.687 19.824
maaslin3 8.979 0.547 10.226
maaslin_contrast_test 7.479 0.691 9.544
maaslin_write_results 5.981 0.470 6.952
maaslin_write_results_lefse_format 5.460 0.373 6.361
maaslin_fit 5.011 0.554 6.266
* 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/4.6-arm64/Resources/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-11-17 21:43:30.993718 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:43:31.022413 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:43:31.058649 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:43:31.071402 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:43:31.083582 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:43:31.115397 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:43:31.1177 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:43:31.123765 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:43:31.166321 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:43:31.168488 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:43:31.185713 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:43:31.20326 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:43:31.207456 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:43:31.222144 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:43:31.248283 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:43:38.468681 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:43:38.495085 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:43:38.524975 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:43:38.532743 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:43:38.54521 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:43:38.580481 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:43:38.582645 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:43:38.586881 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:43:38.623256 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:43:38.625237 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:43:38.647617 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:43:38.660741 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:43:38.665894 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:43:38.679017 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:43:38.707464 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:43:40.783 R[39944:63029703] XType: Using static font registry.
2025-11-17 21:43:49.00138 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:43:49.033713 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:43:49.067853 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:43:49.075882 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:43:49.088463 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:43:49.116908 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:43:49.118943 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:43:49.123017 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:43:49.158962 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:43:49.16107 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:43:49.178294 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:43:49.193149 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:43:49.197458 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:43:49.215108 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:43:49.242942 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:43:55.014097 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:43:55.057729 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:43:55.086582 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:43:55.095737 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:43:55.110614 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:43:55.137909 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:43:55.139889 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:43:55.14382 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:43:55.185254 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:43:55.187592 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:43:55.205501 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:43:55.219083 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:43:55.223324 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:43:55.237422 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:43:55.262135 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:43:55.343936 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/residuals_linear.rds
2025-11-17 21:43:55.381176 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/fitted_linear.rds
2025-11-17 21:43:55.415832 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/residuals_logistic.rds
2025-11-17 21:43:55.598 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/fitted_logistic.rds
2025-11-17 21:44:05.162983 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:44:05.203467 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:44:05.235834 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:44:05.245954 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:44:05.26114 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:44:05.288364 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:44:05.290434 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:44:05.294557 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:44:05.328298 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:44:05.330675 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:44:05.348952 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:44:05.36419 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:44:05.368477 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:44:05.38332 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:44:05.40839 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:44:10.707654 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:44:10.738133 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:44:10.769948 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:44:10.779014 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:44:10.79149 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:44:10.822008 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:44:10.832083 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:44:10.837176 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:44:10.875594 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:44:10.877729 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:44:10.895486 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:44:10.912026 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:44:10.916318 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:44:10.933583 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:44:10.96735 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:44:11.072837 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/residuals_linear.rds
2025-11-17 21:44:11.111076 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/fitted_linear.rds
2025-11-17 21:44:11.146118 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/residuals_logistic.rds
2025-11-17 21:44:11.33055 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/fitted_logistic.rds
2025-11-17 21:44:20.549854 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:44:20.579151 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:44:20.614866 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:44:20.622908 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:44:20.636674 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:44:20.681714 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:44:20.683893 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:44:20.694309 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:44:20.734575 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:44:20.736892 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:44:20.75474 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:44:20.768815 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:44:20.773497 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:44:20.78926 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:44:20.818625 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:44:26.185347 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:44:26.213936 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:44:26.241189 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:44:26.248556 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:44:26.259886 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:44:26.286094 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:44:26.288239 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:44:26.296125 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:44:26.333601 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:44:26.335823 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:44:26.353187 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:44:26.367556 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:44:26.371791 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:44:26.389296 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:44:26.419299 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:44:26.501629 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/residuals_linear.rds
2025-11-17 21:44:26.5408 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/fitted_linear.rds
2025-11-17 21:44:26.580056 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/residuals_logistic.rds
2025-11-17 21:44:26.775553 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c082df91235/fits/fitted_logistic.rds
2025-11-17 21:44:35.943133 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:44:35.972324 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:44:36.006422 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:44:36.015419 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:44:36.027594 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:44:36.058203 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:44:36.060391 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:44:36.064982 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:44:36.106174 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:44:36.108434 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:44:36.129164 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:44:36.144993 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:44:36.149489 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:44:36.163074 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:44:36.186572 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:44:41.630825 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:44:41.664699 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:44:41.692628 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:44:41.700504 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:44:41.748198 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:44:41.781442 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:44:41.783453 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:44:41.787408 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:44:41.825249 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:44:41.827762 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:44:41.845079 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:44:41.862234 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:44:41.866882 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:44:41.881395 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:44:41.906551 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:44:52.231493 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:44:56.380945 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:06.999478 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:11.06087 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:11.283682 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_linear.rds
2025-11-17 21:45:11.319144 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_linear.rds
2025-11-17 21:45:11.342314 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_logistic.rds
2025-11-17 21:45:11.395495 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_logistic.rds
2025-11-17 21:45:21.906384 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:24.727733 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:24.89464 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_linear.rds
2025-11-17 21:45:24.931443 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_linear.rds
2025-11-17 21:45:24.958059 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_logistic.rds
2025-11-17 21:45:24.999893 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_logistic.rds
2025-11-17 21:45:33.30994 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:36.104574 WARNING::Fitting problem for feature 124 returning NA
2025-11-17 21:45:36.242411 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_linear.rds
2025-11-17 21:45:36.280082 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_linear.rds
2025-11-17 21:45:36.310668 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_logistic.rds
2025-11-17 21:45:36.354035 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_logistic.rds
2025-11-17 21:45:44.435804 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:45:44.464693 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:45:44.493157 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:45:44.516343 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:45:44.531366 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:45:44.561748 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:45:44.563817 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:45:44.567903 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:45:44.603645 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:45:44.60623 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:45:44.629038 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:45:44.643776 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:45:44.647985 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:45:44.661549 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:45:44.685544 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:45:50.072463 WARNING::Fitting problem for feature 50 returning NA
2025-11-17 21:45:50.108145 WARNING::Fitting problem for feature 62 returning NA
2025-11-17 21:45:50.133197 WARNING::Fitting problem for feature 74 returning NA
2025-11-17 21:45:50.140813 WARNING::Fitting problem for feature 78 returning NA
2025-11-17 21:45:50.152742 WARNING::Fitting problem for feature 84 returning NA
2025-11-17 21:45:50.183379 WARNING::Fitting problem for feature 96 returning NA
2025-11-17 21:45:50.185546 WARNING::Fitting problem for feature 97 returning NA
2025-11-17 21:45:50.189725 WARNING::Fitting problem for feature 99 returning NA
2025-11-17 21:45:50.223613 WARNING::Fitting problem for feature 114 returning NA
2025-11-17 21:45:50.226365 WARNING::Fitting problem for feature 115 returning NA
2025-11-17 21:45:50.244751 WARNING::Fitting problem for feature 123 returning NA
2025-11-17 21:45:50.266411 WARNING::Fitting problem for feature 130 returning NA
2025-11-17 21:45:50.271412 WARNING::Fitting problem for feature 132 returning NA
2025-11-17 21:45:50.289087 WARNING::Fitting problem for feature 139 returning NA
2025-11-17 21:45:50.314734 WARNING::Fitting problem for feature 150 returning NA
2025-11-17 21:45:50.428382 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_linear.rds
2025-11-17 21:45:50.473026 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_linear.rds
2025-11-17 21:45:50.508756 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/residuals_logistic.rds
2025-11-17 21:45:50.696665 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08d736e9b/fits/fitted_logistic.rds
2025-11-17 21:45:59.515741 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-17 21:45:59.522788 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-17 21:45:59.527808 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-17 21:45:59.548428 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-17 21:45:59.554478 ERROR::Effect name not found in metadata: d
2025-11-17 21:45:59.558195 ERROR::No user formula provided
2025-11-17 21:45:59.569021 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-17 21:45:59.573315 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-17 21:46:00.744494 INFO::Writing function arguments to log file
2025-11-17 21:46:00.751063 INFO::Verifying options selected are valid
2025-11-17 21:46:01.720829 INFO::Writing function arguments to log file
2025-11-17 21:46:01.726089 INFO::Verifying options selected are valid
2025-11-17 21:46:01.726511 INFO::Determining format of input files
2025-11-17 21:46:01.726871 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-17 21:46:01.727769 INFO::Running selected normalization method: TSS
2025-11-17 21:46:01.728336 INFO::Creating output feature tables folder
2025-11-17 21:46:01.728783 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/features/data_norm.tsv
2025-11-17 21:46:01.729417 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-17 21:46:01.729731 INFO::Total samples in data: 16
2025-11-17 21:46:01.730027 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-17 21:46:01.730332 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-17 21:46:01.731017 INFO::Total filtered features: 0
2025-11-17 21:46:01.731367 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-17 21:46:01.731764 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-17 21:46:01.732094 INFO::Filtered feature names from variance filtering:
2025-11-17 21:46:01.732412 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/features/filtered_data.tsv
2025-11-17 21:46:01.733014 INFO::Running selected transform method: LOG
2025-11-17 21:46:01.733433 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/features/data_transformed.tsv
2025-11-17 21:46:01.734068 INFO::Applying z-score to standardize continuous metadata
2025-11-17 21:46:01.736111 INFO::Running the linear model component
2025-11-17 21:46:01.741873 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:01.743683 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:01.745202 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:01.747941 INFO::Counting total values for each feature
2025-11-17 21:46:01.748685 INFO::Running the logistic model component
2025-11-17 21:46:01.754269 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:01.756739 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:01.758789 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:01.762066 INFO::Counting total values for each feature
2025-11-17 21:46:01.762993 INFO::Re-running abundances for warn_prevalence
2025-11-17 21:46:01.763405 INFO::Running selected normalization method: TSS
2025-11-17 21:46:01.763957 INFO::Running selected transform method: LOG
2025-11-17 21:46:01.771123 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:01.772779 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:01.774302 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:01.80744 INFO::Creating fits folder
2025-11-17 21:46:01.808113 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/fits/residuals_linear.rds
2025-11-17 21:46:01.808842 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/fits/fitted_linear.rds
2025-11-17 21:46:01.809388 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/fits/residuals_logistic.rds
2025-11-17 21:46:01.809936 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/fits/fitted_logistic.rds
2025-11-17 21:46:01.81114 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/all_results.tsv
2025-11-17 21:46:01.81193 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/significant_results.tsv
2025-11-17 21:46:01.812559 INFO::Creating output figures folder
2025-11-17 21:46:01.813186 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/figures/summary_plot.pdf
2025-11-17 21:46:02.464511 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/figures
2025-11-17 21:46:02.465375 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-17 21:46:02.467405 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-17 21:46:02.684222 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/figures/summary_plot.pdf
2025-11-17 21:46:03.31826 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c084ec883fc/figures
2025-11-17 21:46:03.318883 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-17 21:46:03.320819 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-17 21:46:03.542516 INFO::Running the linear model component
2025-11-17 21:46:03.545502 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:03.546928 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:03.54813 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:03.550407 INFO::Counting total values for each feature
2025-11-17 21:46:03.550942 INFO::Running the logistic model component
2025-11-17 21:46:03.553475 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:03.555291 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:03.556926 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:03.559487 INFO::Counting total values for each feature
2025-11-17 21:46:03.560162 INFO::Re-running abundances for warn_prevalence
2025-11-17 21:46:03.560396 INFO::Running selected normalization method: TSS
2025-11-17 21:46:03.560824 INFO::Running selected transform method: LOG
2025-11-17 21:46:03.563457 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:03.564751 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:03.565897 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:03.593562 INFO::Creating output folder
2025-11-17 21:46:03.594076 INFO::Creating output figures folder
2025-11-17 21:46:03.594556 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c081550a0a9/figures/summary_plot.pdf
2025-11-17 21:46:04.2429 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c081550a0a9/figures
2025-11-17 21:46:04.243762 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-17 21:46:04.245946 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-17 21:46:04.748688 INFO::Applying z-score to standardize continuous metadata
2025-11-17 21:46:04.75173 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-17 21:46:04.752059 INFO::Bypass z-score application to metadata
2025-11-17 21:46:04.75293 INFO::Bypass z-score application to metadata
2025-11-17 21:46:04.760296 INFO::Determining format of input files
2025-11-17 21:46:04.760597 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-17 21:46:04.760847 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-17 21:46:04.76304 INFO::Determining format of input files
2025-11-17 21:46:04.763359 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-17 21:46:04.766062 INFO::Input format is feature_specific_covariate samples as columns
2025-11-17 21:46:04.768653 INFO::Determining format of input files
2025-11-17 21:46:04.768939 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-17 21:46:04.769242 INFO::Input format is feature_specific_covariate samples as columns
2025-11-17 21:46:04.769711 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-17 21:46:04.769932 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-17 21:46:04.773806 INFO::Running selected transform method: LOG
2025-11-17 21:46:04.774195 INFO::Creating output feature tables folder
2025-11-17 21:46:04.774643 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08633c9ce/features/data_transformed.tsv
2025-11-17 21:46:04.776065 INFO::Running selected transform method: LOG
2025-11-17 21:46:04.776413 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08633c9ce/features/data_transformed.tsv
2025-11-17 21:46:04.77768 INFO::Running selected transform method: PLOG
2025-11-17 21:46:04.778179 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08633c9ce/features/data_transformed.tsv
2025-11-17 21:46:04.779103 INFO::Running selected transform method: NONE
2025-11-17 21:46:04.779344 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c08633c9ce/features/data_transformed.tsv
2025-11-17 21:46:04.78506 INFO::Running the linear model component
2025-11-17 21:46:04.78766 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:04.78903 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:04.790203 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:04.792978 INFO::Counting total values for each feature
2025-11-17 21:46:04.793612 INFO::Running the logistic model component
2025-11-17 21:46:04.796511 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:04.79897 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:04.800797 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:04.803669 INFO::Counting total values for each feature
2025-11-17 21:46:04.804343 INFO::Re-running abundances for warn_prevalence
2025-11-17 21:46:04.804578 INFO::Running selected normalization method: TSS
2025-11-17 21:46:04.805022 INFO::Running selected transform method: LOG
2025-11-17 21:46:04.807783 INFO::Fitting model to feature number 1, a
2025-11-17 21:46:04.809094 INFO::Fitting model to feature number 2, b
2025-11-17 21:46:04.810353 INFO::Fitting model to feature number 3, c
2025-11-17 21:46:04.851888 INFO::Creating output folder
2025-11-17 21:46:04.852388 INFO::Creating fits folder
2025-11-17 21:46:04.852757 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c083205f690/fits/residuals_linear.rds
2025-11-17 21:46:04.853276 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c083205f690/fits/fitted_linear.rds
2025-11-17 21:46:04.853721 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c083205f690/fits/residuals_logistic.rds
2025-11-17 21:46:04.854172 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c083205f690/fits/fitted_logistic.rds
2025-11-17 21:46:04.855265 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c083205f690/all_results.tsv
2025-11-17 21:46:04.855904 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): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDn6bZm/file9c083205f690/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
143.464 4.115 159.061
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.979 | 0.547 | 10.226 | |
| maaslin_check_arguments | 0.064 | 0.002 | 0.070 | |
| maaslin_check_formula | 0.063 | 0.004 | 0.068 | |
| maaslin_compute_formula | 0.064 | 0.006 | 0.075 | |
| maaslin_contrast_test | 7.479 | 0.691 | 9.544 | |
| maaslin_filter | 0.233 | 0.020 | 0.263 | |
| maaslin_fit | 5.011 | 0.554 | 6.266 | |
| maaslin_log_arguments | 0.071 | 0.005 | 0.089 | |
| maaslin_normalize | 0.132 | 0.025 | 0.207 | |
| maaslin_plot_results | 16.885 | 0.687 | 19.824 | |
| maaslin_plot_results_from_output | 16.988 | 0.702 | 18.767 | |
| maaslin_process_metadata | 0.237 | 0.017 | 0.281 | |
| maaslin_read_data | 0.057 | 0.003 | 0.074 | |
| maaslin_reorder_data | 0.062 | 0.004 | 0.068 | |
| maaslin_transform | 0.327 | 0.023 | 0.385 | |
| maaslin_write_results | 5.981 | 0.470 | 6.952 | |
| maaslin_write_results_lefse_format | 5.460 | 0.373 | 6.361 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.004 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |