William Nickols
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 Jan 2026) |
| 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 2026-01-24 11:35 -0500 (Sat, 24 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 1164/2345 | 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: 2026-01-23 20:45:18 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 20:50:45 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 327.4 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
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 17.410 0.711 19.370
maaslin_plot_results 16.835 0.707 18.930
maaslin3 8.951 0.532 10.157
maaslin_contrast_test 6.763 0.566 7.891
maaslin_write_results_lefse_format 5.915 0.349 6.960
maaslin_write_results 5.636 0.573 6.931
maaslin_fit 5.142 0.615 6.207
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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")
2026-01-23 20:48:06.113502 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:06.143721 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:06.176592 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:06.186508 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:06.203555 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:06.229944 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:06.231969 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:06.236408 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:06.28171 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:06.283798 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:06.306692 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:06.320971 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:06.326474 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:06.343983 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:06.377875 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:48:13.580451 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:13.629107 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:13.65498 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:13.663165 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:13.681876 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:13.71107 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:13.713173 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:13.717558 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:13.75533 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:13.767949 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:13.786009 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:13.799994 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:13.804184 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:13.817858 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:13.84823 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:48:15.629 R[40149:830307964] XType: Using static font registry.
2026-01-23 20:48:24.517907 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:24.554182 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:24.585407 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:24.60388 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:24.619832 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:24.649176 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:24.65199 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:24.656417 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:24.695281 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:24.697434 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:24.714937 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:24.729545 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:24.735029 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:24.749469 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:24.776039 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:48:30.319734 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:30.350827 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:30.37895 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:30.387178 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:30.407119 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:30.433447 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:30.435607 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:30.44271 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:30.478613 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:30.489044 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:30.51241 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:30.532075 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:30.537881 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:30.566872 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:30.595564 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:48:30.683047 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/residuals_linear.rds
2026-01-23 20:48:30.721443 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/fitted_linear.rds
2026-01-23 20:48:30.767761 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/residuals_logistic.rds
2026-01-23 20:48:31.011819 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/fitted_logistic.rds
2026-01-23 20:48:40.482976 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:40.510757 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:40.537278 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:40.545073 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:40.557546 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:40.596667 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:40.599006 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:40.603338 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:40.638396 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:40.640654 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:40.660903 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:40.685578 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:40.691278 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:40.711013 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:40.829521 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:48:47.095648 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:47.125839 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:47.18257 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:47.190226 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:47.202842 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:47.230432 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:47.232685 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:47.23703 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:47.274134 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:47.27632 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:47.295251 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:47.310332 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:47.314846 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:47.3289 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:47.358417 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:48:47.437111 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/residuals_linear.rds
2026-01-23 20:48:47.47386 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/fitted_linear.rds
2026-01-23 20:48:47.513681 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/residuals_logistic.rds
2026-01-23 20:48:47.739114 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/fitted_logistic.rds
2026-01-23 20:48:57.423499 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:48:57.457968 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:48:57.486878 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:48:57.502443 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:48:57.517891 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:48:57.566806 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:48:57.569347 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:48:57.574184 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:48:57.611371 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:48:57.613903 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:48:57.639555 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:48:57.661503 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:48:57.667809 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:48:57.681376 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:48:57.706357 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:49:03.02109 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:49:03.050333 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:49:03.085557 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:49:03.094895 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:49:03.107595 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:49:03.136247 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:49:03.141472 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:49:03.147612 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:49:03.193232 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:49:03.195394 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:49:03.21369 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:49:03.228604 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:49:03.233129 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:49:03.270856 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:49:03.299702 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:49:03.378182 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/residuals_linear.rds
2026-01-23 20:49:03.432724 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/fitted_linear.rds
2026-01-23 20:49:03.470539 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/residuals_logistic.rds
2026-01-23 20:49:03.699185 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53ab382a4/fits/fitted_logistic.rds
2026-01-23 20:49:12.895163 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:49:12.929473 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:49:12.96006 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:49:12.975131 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:49:12.989397 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:49:13.022494 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:49:13.024646 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:49:13.029523 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:49:13.069483 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:49:13.071898 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:49:13.092695 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:49:13.111667 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:49:13.116809 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:49:13.155961 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:49:13.180927 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:49:18.580396 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:49:18.613638 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:49:18.642931 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:49:18.650994 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:49:18.663244 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:49:18.690661 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:49:18.692823 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:49:18.69728 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:49:18.740356 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:49:18.742709 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:49:18.766444 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:49:18.784972 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:49:18.78912 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:49:18.80411 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:49:18.828876 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:49:28.979973 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:49:33.185678 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:49:43.634032 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:49:47.641973 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:49:47.86109 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_linear.rds
2026-01-23 20:49:47.896601 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_linear.rds
2026-01-23 20:49:47.920713 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_logistic.rds
2026-01-23 20:49:47.964189 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_logistic.rds
2026-01-23 20:49:57.633549 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:50:00.408042 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:50:00.508934 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_linear.rds
2026-01-23 20:50:00.54166 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_linear.rds
2026-01-23 20:50:00.563507 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_logistic.rds
2026-01-23 20:50:00.607468 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_logistic.rds
2026-01-23 20:50:08.702649 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:50:11.616402 WARNING::Fitting problem for feature 124 returning NA
2026-01-23 20:50:11.726134 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_linear.rds
2026-01-23 20:50:11.767004 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_linear.rds
2026-01-23 20:50:11.79357 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_logistic.rds
2026-01-23 20:50:11.834154 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_logistic.rds
2026-01-23 20:50:19.840984 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:50:19.869598 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:50:19.896555 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:50:19.904444 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:50:19.916377 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:50:19.946196 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:50:19.94836 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:50:19.952803 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:50:19.987716 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:50:19.99028 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:50:20.0098 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:50:20.02486 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:50:20.029618 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:50:20.044094 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:50:20.068964 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:50:25.647567 WARNING::Fitting problem for feature 50 returning NA
2026-01-23 20:50:25.675374 WARNING::Fitting problem for feature 62 returning NA
2026-01-23 20:50:25.702529 WARNING::Fitting problem for feature 74 returning NA
2026-01-23 20:50:25.710736 WARNING::Fitting problem for feature 78 returning NA
2026-01-23 20:50:25.730792 WARNING::Fitting problem for feature 84 returning NA
2026-01-23 20:50:25.759604 WARNING::Fitting problem for feature 96 returning NA
2026-01-23 20:50:25.761781 WARNING::Fitting problem for feature 97 returning NA
2026-01-23 20:50:25.765961 WARNING::Fitting problem for feature 99 returning NA
2026-01-23 20:50:25.801192 WARNING::Fitting problem for feature 114 returning NA
2026-01-23 20:50:25.803374 WARNING::Fitting problem for feature 115 returning NA
2026-01-23 20:50:25.821609 WARNING::Fitting problem for feature 123 returning NA
2026-01-23 20:50:25.838046 WARNING::Fitting problem for feature 130 returning NA
2026-01-23 20:50:25.842274 WARNING::Fitting problem for feature 132 returning NA
2026-01-23 20:50:25.857244 WARNING::Fitting problem for feature 139 returning NA
2026-01-23 20:50:25.883 WARNING::Fitting problem for feature 150 returning NA
2026-01-23 20:50:25.983236 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_linear.rds
2026-01-23 20:50:26.027493 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_linear.rds
2026-01-23 20:50:26.068323 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/residuals_logistic.rds
2026-01-23 20:50:26.267447 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51e42905/fits/fitted_logistic.rds
2026-01-23 20:50:35.052535 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2026-01-23 20:50:35.061247 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2026-01-23 20:50:35.065569 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2026-01-23 20:50:35.084194 ERROR::No fixed, group, or
ordered effects included in formula.
2026-01-23 20:50:35.089742 ERROR::Effect name not found in metadata: d
2026-01-23 20:50:35.099404 ERROR::No user formula provided
2026-01-23 20:50:35.110207 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2026-01-23 20:50:35.114341 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2026-01-23 20:50:36.294111 INFO::Writing function arguments to log file
2026-01-23 20:50:36.300856 INFO::Verifying options selected are valid
2026-01-23 20:50:37.273012 INFO::Writing function arguments to log file
2026-01-23 20:50:37.27829 INFO::Verifying options selected are valid
2026-01-23 20:50:37.278702 INFO::Determining format of input files
2026-01-23 20:50:37.279052 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-23 20:50:37.279923 INFO::Running selected normalization method: TSS
2026-01-23 20:50:37.280498 INFO::Creating output feature tables folder
2026-01-23 20:50:37.280911 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/features/data_norm.tsv
2026-01-23 20:50:37.281519 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2026-01-23 20:50:37.281833 INFO::Total samples in data: 16
2026-01-23 20:50:37.282134 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2026-01-23 20:50:37.282433 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2026-01-23 20:50:37.283108 INFO::Total filtered features: 0
2026-01-23 20:50:37.283471 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2026-01-23 20:50:37.283878 INFO::Total features filtered by non-zero variance filtering: 0
2026-01-23 20:50:37.284227 INFO::Filtered feature names from variance filtering:
2026-01-23 20:50:37.284539 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/features/filtered_data.tsv
2026-01-23 20:50:37.285154 INFO::Running selected transform method: LOG
2026-01-23 20:50:37.285556 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/features/data_transformed.tsv
2026-01-23 20:50:37.286187 INFO::Applying z-score to standardize continuous metadata
2026-01-23 20:50:37.287883 INFO::Running the linear model component
2026-01-23 20:50:37.293907 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:37.29554 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:37.296974 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:37.301391 INFO::Counting total values for each feature
2026-01-23 20:50:37.302273 INFO::Running the logistic model component
2026-01-23 20:50:37.308496 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:37.310973 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:37.313124 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:37.316635 INFO::Counting total values for each feature
2026-01-23 20:50:37.317544 INFO::Re-running abundances for warn_prevalence
2026-01-23 20:50:37.317977 INFO::Running selected normalization method: TSS
2026-01-23 20:50:37.318536 INFO::Running selected transform method: LOG
2026-01-23 20:50:37.323992 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:37.326562 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:37.328175 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:37.354517 INFO::Creating fits folder
2026-01-23 20:50:37.355263 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/fits/residuals_linear.rds
2026-01-23 20:50:37.355938 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/fits/fitted_linear.rds
2026-01-23 20:50:37.356478 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/fits/residuals_logistic.rds
2026-01-23 20:50:37.357065 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/fits/fitted_logistic.rds
2026-01-23 20:50:37.358233 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/all_results.tsv
2026-01-23 20:50:37.359112 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//RtmpIpxhJf/file9cd51468ab7/significant_results.tsv
2026-01-23 20:50:37.359733 INFO::Creating output figures folder
2026-01-23 20:50:37.360398 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/figures/summary_plot.pdf
2026-01-23 20:50:38.017038 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/figures
2026-01-23 20:50:38.017924 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-23 20:50:38.020118 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-23 20:50:38.240512 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/figures/summary_plot.pdf
2026-01-23 20:50:38.891741 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd51468ab7/figures
2026-01-23 20:50:38.892484 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-23 20:50:38.894738 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-23 20:50:39.104188 INFO::Running the linear model component
2026-01-23 20:50:39.107101 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:39.109585 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:39.110882 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:39.113323 INFO::Counting total values for each feature
2026-01-23 20:50:39.113895 INFO::Running the logistic model component
2026-01-23 20:50:39.116526 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:39.118638 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:39.120459 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:39.123256 INFO::Counting total values for each feature
2026-01-23 20:50:39.123943 INFO::Re-running abundances for warn_prevalence
2026-01-23 20:50:39.124185 INFO::Running selected normalization method: TSS
2026-01-23 20:50:39.124614 INFO::Running selected transform method: LOG
2026-01-23 20:50:39.127274 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:39.12863 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:39.129847 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:39.163839 INFO::Creating output folder
2026-01-23 20:50:39.164356 INFO::Creating output figures folder
2026-01-23 20:50:39.164874 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd543c645bb/figures/summary_plot.pdf
2026-01-23 20:50:39.830757 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd543c645bb/figures
2026-01-23 20:50:39.831434 INFO::Plotting associations from most to least significant, grouped by metadata
2026-01-23 20:50:39.833381 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2026-01-23 20:50:40.27996 INFO::Applying z-score to standardize continuous metadata
2026-01-23 20:50:40.283126 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2026-01-23 20:50:40.283449 INFO::Bypass z-score application to metadata
2026-01-23 20:50:40.284357 INFO::Bypass z-score application to metadata
2026-01-23 20:50:40.292323 INFO::Determining format of input files
2026-01-23 20:50:40.292631 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-23 20:50:40.29288 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2026-01-23 20:50:40.295139 INFO::Determining format of input files
2026-01-23 20:50:40.295461 INFO::Input format is data samples as columns and metadata samples as rows
2026-01-23 20:50:40.29584 INFO::Input format is feature_specific_covariate samples as columns
2026-01-23 20:50:40.298293 INFO::Determining format of input files
2026-01-23 20:50:40.298576 INFO::Input format is data samples as rows and metadata samples as rows
2026-01-23 20:50:40.298874 INFO::Input format is feature_specific_covariate samples as columns
2026-01-23 20:50:40.299329 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2026-01-23 20:50:40.299543 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2026-01-23 20:50:40.303432 INFO::Running selected transform method: LOG
2026-01-23 20:50:40.303788 INFO::Creating output feature tables folder
2026-01-23 20:50:40.30414 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd555cdb4cc/features/data_transformed.tsv
2026-01-23 20:50:40.305537 INFO::Running selected transform method: LOG
2026-01-23 20:50:40.305861 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd555cdb4cc/features/data_transformed.tsv
2026-01-23 20:50:40.30708 INFO::Running selected transform method: PLOG
2026-01-23 20:50:40.307575 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd555cdb4cc/features/data_transformed.tsv
2026-01-23 20:50:40.308505 INFO::Running selected transform method: NONE
2026-01-23 20:50:40.308748 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd555cdb4cc/features/data_transformed.tsv
2026-01-23 20:50:40.311579 INFO::Running the linear model component
2026-01-23 20:50:40.314191 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:40.315544 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:40.316713 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:40.31894 INFO::Counting total values for each feature
2026-01-23 20:50:40.319467 INFO::Running the logistic model component
2026-01-23 20:50:40.322036 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:40.324049 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:40.325767 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:40.328382 INFO::Counting total values for each feature
2026-01-23 20:50:40.32901 INFO::Re-running abundances for warn_prevalence
2026-01-23 20:50:40.329241 INFO::Running selected normalization method: TSS
2026-01-23 20:50:40.329649 INFO::Running selected transform method: LOG
2026-01-23 20:50:40.332236 INFO::Fitting model to feature number 1, a
2026-01-23 20:50:40.333464 INFO::Fitting model to feature number 2, b
2026-01-23 20:50:40.334622 INFO::Fitting model to feature number 3, c
2026-01-23 20:50:40.358409 INFO::Creating output folder
2026-01-23 20:50:40.358825 INFO::Creating fits folder
2026-01-23 20:50:40.359119 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53418e916/fits/residuals_linear.rds
2026-01-23 20:50:40.359893 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53418e916/fits/fitted_linear.rds
2026-01-23 20:50:40.36114 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53418e916/fits/residuals_logistic.rds
2026-01-23 20:50:40.361807 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53418e916/fits/fitted_logistic.rds
2026-01-23 20:50:40.362988 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpIpxhJf/file9cd53418e916/all_results.tsv
2026-01-23 20:50:40.364141 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//RtmpIpxhJf/file9cd53418e916/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
143.764 4.516 159.779
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.951 | 0.532 | 10.157 | |
| maaslin_check_arguments | 0.054 | 0.002 | 0.060 | |
| maaslin_check_formula | 0.059 | 0.004 | 0.071 | |
| maaslin_compute_formula | 0.064 | 0.004 | 0.076 | |
| maaslin_contrast_test | 6.763 | 0.566 | 7.891 | |
| maaslin_filter | 0.219 | 0.021 | 0.254 | |
| maaslin_fit | 5.142 | 0.615 | 6.207 | |
| maaslin_log_arguments | 0.065 | 0.004 | 0.072 | |
| maaslin_normalize | 0.134 | 0.011 | 0.161 | |
| maaslin_plot_results | 16.835 | 0.707 | 18.930 | |
| maaslin_plot_results_from_output | 17.410 | 0.711 | 19.370 | |
| maaslin_process_metadata | 0.229 | 0.018 | 0.267 | |
| maaslin_read_data | 0.053 | 0.003 | 0.066 | |
| maaslin_reorder_data | 0.056 | 0.003 | 0.063 | |
| maaslin_transform | 0.286 | 0.027 | 0.350 | |
| maaslin_write_results | 5.636 | 0.573 | 6.931 | |
| maaslin_write_results_lefse_format | 5.915 | 0.349 | 6.960 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.002 | |