William Nickols
| Snapshot Date: 2025-12-05 13:40 -0500 (Fri, 05 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 2025-12-06 11:35 -0500 (Sat, 06 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1157/2331 | 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: /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: 2025-12-05 20:41:37 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 20:46:58 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 321.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 17.104 0.770 18.892
maaslin_plot_results_from_output 17.280 0.524 18.638
maaslin3 8.606 0.527 10.156
maaslin_contrast_test 7.378 0.631 8.679
maaslin_write_results 6.196 0.403 6.909
maaslin_write_results_lefse_format 5.908 0.518 6.844
maaslin_fit 5.120 0.618 6.166
* 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")
2025-12-05 20:44:23.461342 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:44:23.492639 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:44:23.529226 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:44:23.537072 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:44:23.549548 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:44:23.577027 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:44:23.584068 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:44:23.588323 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:44:23.622675 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:44:23.624708 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:44:23.64151 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:44:23.659592 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:44:23.663645 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:44:23.677447 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:44:23.701395 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:44:30.513307 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:44:30.541577 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:44:30.573021 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:44:30.581168 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:44:30.593664 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:44:30.630961 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:44:30.633515 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:44:30.638553 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:44:30.672123 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:44:30.674437 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:44:30.691498 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:44:30.728424 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:44:30.733956 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:44:30.749523 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:44:30.774192 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:44:32.407 R[59818:295572728] XType: Using static font registry.
2025-12-05 20:44:41.078185 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:44:41.108375 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:44:41.135862 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:44:41.144632 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:44:41.158186 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:44:41.186902 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:44:41.188935 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:44:41.192876 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:44:41.239295 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:44:41.241496 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:44:41.259309 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:44:41.275444 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:44:41.280773 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:44:41.295721 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:44:41.321275 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:44:46.888463 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:44:46.930333 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:44:46.964677 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:44:46.973299 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:44:46.985851 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:44:47.013865 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:44:47.015909 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:44:47.026646 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:44:47.06254 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:44:47.064667 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:44:47.081844 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:44:47.095581 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:44:47.099751 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:44:47.113587 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:44:47.139219 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:44:47.22246 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/residuals_linear.rds
2025-12-05 20:44:47.259683 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/fitted_linear.rds
2025-12-05 20:44:47.294146 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/residuals_logistic.rds
2025-12-05 20:44:47.479591 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/fitted_logistic.rds
2025-12-05 20:44:57.136435 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:44:57.166933 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:44:57.19483 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:44:57.20225 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:44:57.214572 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:44:57.242897 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:44:57.244961 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:44:57.249888 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:44:57.283692 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:44:57.285639 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:44:57.302174 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:44:57.315639 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:44:57.319829 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:44:57.333599 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:44:57.359854 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:45:02.919782 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:45:02.945856 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:45:02.971768 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:45:02.979705 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:45:02.992826 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:45:03.021798 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:45:03.023976 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:45:03.028645 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:45:03.063233 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:45:03.065446 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:45:03.086317 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:45:03.102015 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:45:03.106479 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:45:03.12086 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:45:03.147882 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:45:03.238236 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/residuals_linear.rds
2025-12-05 20:45:03.275356 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/fitted_linear.rds
2025-12-05 20:45:03.311536 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/residuals_logistic.rds
2025-12-05 20:45:03.505086 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/fitted_logistic.rds
2025-12-05 20:45:12.361234 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:45:12.39204 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:45:12.418649 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:45:12.426954 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:45:12.439203 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:45:12.469823 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:45:12.471858 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:45:12.475946 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:45:12.606339 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:45:12.608643 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:45:12.626054 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:45:12.642644 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:45:12.647872 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:45:12.668767 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:45:12.693052 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:45:17.908817 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:45:17.938376 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:45:17.965977 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:45:17.973833 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:45:17.986309 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:45:18.014506 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:45:18.017032 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:45:18.022276 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:45:18.057216 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:45:18.059371 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:45:18.077528 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:45:18.094445 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:45:18.099717 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:45:18.115238 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:45:18.141588 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:45:18.229175 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/residuals_linear.rds
2025-12-05 20:45:18.285418 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/fitted_linear.rds
2025-12-05 20:45:18.321239 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/residuals_logistic.rds
2025-12-05 20:45:18.504141 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa23be14d0/fits/fitted_logistic.rds
2025-12-05 20:45:27.45979 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:45:27.488078 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:45:27.51762 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:45:27.526127 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:45:27.540897 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:45:27.570152 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:45:27.572308 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:45:27.576631 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:45:27.620309 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:45:27.622738 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:45:27.659733 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:45:27.674201 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:45:27.678787 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:45:27.694092 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:45:27.72398 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:45:33.007491 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:45:33.035649 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:45:33.062419 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:45:33.071467 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:45:33.083926 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:45:33.12109 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:45:33.123194 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:45:33.127559 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:45:33.188787 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:45:33.190891 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:45:33.212322 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:45:33.226794 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:45:33.231183 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:45:33.246589 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:45:33.272124 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:45:43.311416 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:45:47.26055 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:45:57.764281 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:46:01.691786 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:46:01.911062 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_linear.rds
2025-12-05 20:46:01.952634 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_linear.rds
2025-12-05 20:46:01.976977 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_logistic.rds
2025-12-05 20:46:02.017987 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_logistic.rds
2025-12-05 20:46:11.656448 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:46:14.527824 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:46:14.653175 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_linear.rds
2025-12-05 20:46:14.696671 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_linear.rds
2025-12-05 20:46:14.719109 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_logistic.rds
2025-12-05 20:46:14.762663 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_logistic.rds
2025-12-05 20:46:22.9851 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:46:25.769251 WARNING::Fitting problem for feature 124 returning NA
2025-12-05 20:46:25.903314 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_linear.rds
2025-12-05 20:46:25.938159 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_linear.rds
2025-12-05 20:46:25.960269 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_logistic.rds
2025-12-05 20:46:26.008044 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_logistic.rds
2025-12-05 20:46:33.778564 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:46:33.806922 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:46:33.833508 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:46:33.84295 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:46:33.856737 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:46:33.883309 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:46:33.885345 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:46:33.889356 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:46:33.947906 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:46:33.950061 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:46:33.967195 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:46:33.982616 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:46:33.987234 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:46:34.002619 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:46:34.029091 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:46:39.308094 WARNING::Fitting problem for feature 50 returning NA
2025-12-05 20:46:39.33672 WARNING::Fitting problem for feature 62 returning NA
2025-12-05 20:46:39.362846 WARNING::Fitting problem for feature 74 returning NA
2025-12-05 20:46:39.370375 WARNING::Fitting problem for feature 78 returning NA
2025-12-05 20:46:39.383877 WARNING::Fitting problem for feature 84 returning NA
2025-12-05 20:46:39.418236 WARNING::Fitting problem for feature 96 returning NA
2025-12-05 20:46:39.42047 WARNING::Fitting problem for feature 97 returning NA
2025-12-05 20:46:39.424712 WARNING::Fitting problem for feature 99 returning NA
2025-12-05 20:46:39.46427 WARNING::Fitting problem for feature 114 returning NA
2025-12-05 20:46:39.467214 WARNING::Fitting problem for feature 115 returning NA
2025-12-05 20:46:39.486413 WARNING::Fitting problem for feature 123 returning NA
2025-12-05 20:46:39.507698 WARNING::Fitting problem for feature 130 returning NA
2025-12-05 20:46:39.512608 WARNING::Fitting problem for feature 132 returning NA
2025-12-05 20:46:39.55133 WARNING::Fitting problem for feature 139 returning NA
2025-12-05 20:46:39.582572 WARNING::Fitting problem for feature 150 returning NA
2025-12-05 20:46:39.68819 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_linear.rds
2025-12-05 20:46:39.723294 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_linear.rds
2025-12-05 20:46:39.761727 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/residuals_logistic.rds
2025-12-05 20:46:39.946776 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa61ab65c9/fits/fitted_logistic.rds
2025-12-05 20:46:48.594791 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-05 20:46:48.60162 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-05 20:46:48.605983 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-05 20:46:48.625615 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-05 20:46:48.631239 ERROR::Effect name not found in metadata: d
2025-12-05 20:46:48.634973 ERROR::No user formula provided
2025-12-05 20:46:48.647264 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-05 20:46:48.652109 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-05 20:46:49.808641 INFO::Writing function arguments to log file
2025-12-05 20:46:49.815104 INFO::Verifying options selected are valid
2025-12-05 20:46:50.774126 INFO::Writing function arguments to log file
2025-12-05 20:46:50.778673 INFO::Verifying options selected are valid
2025-12-05 20:46:50.779037 INFO::Determining format of input files
2025-12-05 20:46:50.779338 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 20:46:50.780119 INFO::Running selected normalization method: TSS
2025-12-05 20:46:50.780629 INFO::Creating output feature tables folder
2025-12-05 20:46:50.781011 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/features/data_norm.tsv
2025-12-05 20:46:50.781591 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-05 20:46:50.781896 INFO::Total samples in data: 16
2025-12-05 20:46:50.782175 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-05 20:46:50.782446 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-05 20:46:50.783085 INFO::Total filtered features: 0
2025-12-05 20:46:50.783413 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-05 20:46:50.783784 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-05 20:46:50.784083 INFO::Filtered feature names from variance filtering:
2025-12-05 20:46:50.784369 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/features/filtered_data.tsv
2025-12-05 20:46:50.784895 INFO::Running selected transform method: LOG
2025-12-05 20:46:50.785291 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/features/data_transformed.tsv
2025-12-05 20:46:50.785882 INFO::Applying z-score to standardize continuous metadata
2025-12-05 20:46:50.788092 INFO::Running the linear model component
2025-12-05 20:46:50.798266 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:50.800143 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:50.801733 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:50.804684 INFO::Counting total values for each feature
2025-12-05 20:46:50.805491 INFO::Running the logistic model component
2025-12-05 20:46:50.812456 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:50.814733 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:50.816707 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:50.821448 INFO::Counting total values for each feature
2025-12-05 20:46:50.82357 INFO::Re-running abundances for warn_prevalence
2025-12-05 20:46:50.824557 INFO::Running selected normalization method: TSS
2025-12-05 20:46:50.82587 INFO::Running selected transform method: LOG
2025-12-05 20:46:50.836668 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:50.838466 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:50.839872 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:50.868319 INFO::Creating fits folder
2025-12-05 20:46:50.868887 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/fits/residuals_linear.rds
2025-12-05 20:46:50.869457 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/fits/fitted_linear.rds
2025-12-05 20:46:50.869925 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/fits/residuals_logistic.rds
2025-12-05 20:46:50.8704 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/fits/fitted_logistic.rds
2025-12-05 20:46:50.871444 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/all_results.tsv
2025-12-05 20:46:50.87217 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//Rtmpu2SDCz/filee9aa6daf4271/significant_results.tsv
2025-12-05 20:46:50.872693 INFO::Creating output figures folder
2025-12-05 20:46:50.873176 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/figures/summary_plot.pdf
2025-12-05 20:46:51.553908 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/figures
2025-12-05 20:46:51.554844 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 20:46:51.556995 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 20:46:51.777421 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/figures/summary_plot.pdf
2025-12-05 20:46:52.544039 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6daf4271/figures
2025-12-05 20:46:52.544661 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 20:46:52.546705 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 20:46:52.767827 INFO::Running the linear model component
2025-12-05 20:46:52.770713 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:52.772216 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:52.775952 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:52.7787 INFO::Counting total values for each feature
2025-12-05 20:46:52.779319 INFO::Running the logistic model component
2025-12-05 20:46:52.782038 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:52.784126 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:52.78595 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:52.788846 INFO::Counting total values for each feature
2025-12-05 20:46:52.789564 INFO::Re-running abundances for warn_prevalence
2025-12-05 20:46:52.789813 INFO::Running selected normalization method: TSS
2025-12-05 20:46:52.790259 INFO::Running selected transform method: LOG
2025-12-05 20:46:52.792951 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:52.794281 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:52.795612 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:52.827064 INFO::Creating output folder
2025-12-05 20:46:52.827545 INFO::Creating output figures folder
2025-12-05 20:46:52.828008 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6bdb144c/figures/summary_plot.pdf
2025-12-05 20:46:53.522424 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa6bdb144c/figures
2025-12-05 20:46:53.523057 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-05 20:46:53.524967 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-05 20:46:53.989235 INFO::Applying z-score to standardize continuous metadata
2025-12-05 20:46:53.992183 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-05 20:46:53.992468 INFO::Bypass z-score application to metadata
2025-12-05 20:46:53.993268 INFO::Bypass z-score application to metadata
2025-12-05 20:46:54.003261 INFO::Determining format of input files
2025-12-05 20:46:54.003622 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 20:46:54.003895 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-05 20:46:54.006481 INFO::Determining format of input files
2025-12-05 20:46:54.006889 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-05 20:46:54.007298 INFO::Input format is feature_specific_covariate samples as columns
2025-12-05 20:46:54.010106 INFO::Determining format of input files
2025-12-05 20:46:54.010468 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-05 20:46:54.010788 INFO::Input format is feature_specific_covariate samples as columns
2025-12-05 20:46:54.011278 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-05 20:46:54.011519 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-05 20:46:54.018324 INFO::Running selected transform method: LOG
2025-12-05 20:46:54.018779 INFO::Creating output feature tables folder
2025-12-05 20:46:54.019174 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa722a5881/features/data_transformed.tsv
2025-12-05 20:46:54.020718 INFO::Running selected transform method: LOG
2025-12-05 20:46:54.02107 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa722a5881/features/data_transformed.tsv
2025-12-05 20:46:54.022393 INFO::Running selected transform method: PLOG
2025-12-05 20:46:54.022961 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa722a5881/features/data_transformed.tsv
2025-12-05 20:46:54.024019 INFO::Running selected transform method: NONE
2025-12-05 20:46:54.024292 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa722a5881/features/data_transformed.tsv
2025-12-05 20:46:54.02751 INFO::Running the linear model component
2025-12-05 20:46:54.030403 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:54.031985 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:54.03334 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:54.035921 INFO::Counting total values for each feature
2025-12-05 20:46:54.036539 INFO::Running the logistic model component
2025-12-05 20:46:54.039249 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:54.041672 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:54.043703 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:54.052152 INFO::Counting total values for each feature
2025-12-05 20:46:54.052967 INFO::Re-running abundances for warn_prevalence
2025-12-05 20:46:54.05324 INFO::Running selected normalization method: TSS
2025-12-05 20:46:54.053687 INFO::Running selected transform method: LOG
2025-12-05 20:46:54.056493 INFO::Fitting model to feature number 1, a
2025-12-05 20:46:54.057958 INFO::Fitting model to feature number 2, b
2025-12-05 20:46:54.05923 INFO::Fitting model to feature number 3, c
2025-12-05 20:46:54.103532 INFO::Creating output folder
2025-12-05 20:46:54.104146 INFO::Creating fits folder
2025-12-05 20:46:54.104492 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa3a18b7b5/fits/residuals_linear.rds
2025-12-05 20:46:54.105012 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa3a18b7b5/fits/fitted_linear.rds
2025-12-05 20:46:54.105486 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa3a18b7b5/fits/residuals_logistic.rds
2025-12-05 20:46:54.105994 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa3a18b7b5/fits/fitted_logistic.rds
2025-12-05 20:46:54.10717 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpu2SDCz/filee9aa3a18b7b5/all_results.tsv
2025-12-05 20:46:54.107878 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//Rtmpu2SDCz/filee9aa3a18b7b5/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.154 4.472 155.844
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.606 | 0.527 | 10.156 | |
| maaslin_check_arguments | 0.061 | 0.002 | 0.063 | |
| maaslin_check_formula | 0.060 | 0.004 | 0.069 | |
| maaslin_compute_formula | 0.064 | 0.003 | 0.069 | |
| maaslin_contrast_test | 7.378 | 0.631 | 8.679 | |
| maaslin_filter | 0.239 | 0.023 | 0.281 | |
| maaslin_fit | 5.120 | 0.618 | 6.166 | |
| maaslin_log_arguments | 0.065 | 0.004 | 0.076 | |
| maaslin_normalize | 0.125 | 0.011 | 0.150 | |
| maaslin_plot_results | 17.104 | 0.770 | 18.892 | |
| maaslin_plot_results_from_output | 17.280 | 0.524 | 18.638 | |
| maaslin_process_metadata | 0.244 | 0.027 | 0.301 | |
| maaslin_read_data | 0.062 | 0.003 | 0.067 | |
| maaslin_reorder_data | 0.061 | 0.003 | 0.073 | |
| maaslin_transform | 0.294 | 0.028 | 0.354 | |
| maaslin_write_results | 6.196 | 0.403 | 6.909 | |
| maaslin_write_results_lefse_format | 5.908 | 0.518 | 6.844 | |
| preprocess_dna_mtx | 0.002 | 0.001 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |