William Nickols
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 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 2025-11-28 11:39 -0500 (Fri, 28 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" | 4866 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 1155/2328 | 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: 2025-11-27 20:51:03 -0500 (Thu, 27 Nov 2025) |
| EndedAt: 2025-11-27 20:56:29 -0500 (Thu, 27 Nov 2025) |
| EllapsedTime: 326.4 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
###
##############################################################################
##############################################################################
* 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 16.958 0.700 18.779
maaslin_plot_results 16.868 0.641 19.093
maaslin3 8.555 0.509 9.620
maaslin_contrast_test 7.430 0.723 8.799
maaslin_write_results 5.876 0.435 6.871
maaslin_write_results_lefse_format 5.477 0.380 6.234
maaslin_fit 5.023 0.600 6.099
* 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")
2025-11-27 20:53:50.652763 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:53:50.681642 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:53:50.721164 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:53:50.729209 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:53:50.742114 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:53:50.777996 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:53:50.780339 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:53:50.784365 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:53:50.816473 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:53:50.818456 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:53:50.834691 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:53:50.852705 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:53:50.856762 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:53:50.869869 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:53:50.897672 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:53:57.755425 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:53:57.78238 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:53:57.817996 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:53:57.838232 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:53:57.851021 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:53:57.878835 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:53:57.881204 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:53:57.885775 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:53:57.926162 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:53:57.928428 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:53:57.945899 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:53:57.966281 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:53:57.97052 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:53:57.985924 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:53:58.015893 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:53:59.716 R[26863:191637451] XType: Using static font registry.
2025-11-27 20:54:08.317356 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:08.34703 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:08.375434 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:08.38298 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:08.394791 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:08.423031 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:08.425641 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:08.430603 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:08.469162 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:08.471193 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:08.488287 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:08.501936 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:08.506438 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:08.522938 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:08.547689 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:54:14.176224 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:14.208356 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:14.253733 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:14.262745 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:14.275253 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:14.30101 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:14.30308 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:14.307574 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:14.343858 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:14.345893 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:14.362761 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:14.376398 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:14.380595 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:14.394107 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:14.4183 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:54:14.493986 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/residuals_linear.rds
2025-11-27 20:54:14.526767 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/fitted_linear.rds
2025-11-27 20:54:14.568298 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/residuals_logistic.rds
2025-11-27 20:54:14.758143 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/fitted_logistic.rds
2025-11-27 20:54:24.30861 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:24.339277 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:24.370585 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:24.378623 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:24.3918 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:24.421806 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:24.424105 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:24.428252 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:24.463994 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:24.466196 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:24.499164 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:24.514537 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:24.51907 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:24.533287 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:24.557474 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:54:30.325368 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:30.351799 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:30.38237 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:30.399249 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:30.413694 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:30.477744 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:30.480955 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:30.485878 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:30.527697 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:30.530289 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:30.548501 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:30.562537 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:30.566874 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:30.580972 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:30.607387 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:54:30.685734 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/residuals_linear.rds
2025-11-27 20:54:30.719858 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/fitted_linear.rds
2025-11-27 20:54:30.757506 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/residuals_logistic.rds
2025-11-27 20:54:30.959592 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/fitted_logistic.rds
2025-11-27 20:54:40.15502 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:40.212059 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:40.258265 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:40.266884 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:40.279764 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:40.319213 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:40.323723 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:40.333087 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:40.377247 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:40.379408 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:40.396999 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:40.410643 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:40.414797 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:40.428426 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:40.462517 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:54:45.818515 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:45.849267 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:45.90019 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:45.907427 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:45.91957 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:45.949357 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:45.95223 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:45.956816 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:46.000033 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:46.002607 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:46.021126 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:46.034843 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:46.039681 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:46.056045 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:46.081316 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:54:46.159197 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/residuals_linear.rds
2025-11-27 20:54:46.194287 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/fitted_linear.rds
2025-11-27 20:54:46.230897 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/residuals_logistic.rds
2025-11-27 20:54:46.433434 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef11af4d3d/fits/fitted_logistic.rds
2025-11-27 20:54:55.689616 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:54:55.772293 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:54:55.800311 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:54:55.807996 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:54:55.81997 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:54:55.845766 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:54:55.847762 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:54:55.852007 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:54:55.88868 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:54:55.890744 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:54:55.909257 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:54:55.92291 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:54:55.927187 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:54:55.944626 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:54:55.96935 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:55:01.291351 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:55:01.321014 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:55:01.380191 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:55:01.387856 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:55:01.399935 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:55:01.430323 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:55:01.432847 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:55:01.437727 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:55:01.471341 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:55:01.473483 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:55:01.491337 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:55:01.510789 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:55:01.515361 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:55:01.533004 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:55:01.557344 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:55:11.954447 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:16.108133 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:26.747512 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:30.810588 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:31.028962 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_linear.rds
2025-11-27 20:55:31.07348 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_linear.rds
2025-11-27 20:55:31.095875 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_logistic.rds
2025-11-27 20:55:31.140088 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_logistic.rds
2025-11-27 20:55:41.600804 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:44.338155 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:44.458367 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_linear.rds
2025-11-27 20:55:44.49768 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_linear.rds
2025-11-27 20:55:44.519928 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_logistic.rds
2025-11-27 20:55:44.563842 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_logistic.rds
2025-11-27 20:55:52.969886 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:55.829755 WARNING::Fitting problem for feature 124 returning NA
2025-11-27 20:55:55.958527 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_linear.rds
2025-11-27 20:55:55.999952 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_linear.rds
2025-11-27 20:55:56.022947 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_logistic.rds
2025-11-27 20:55:56.069221 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_logistic.rds
2025-11-27 20:56:04.244698 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:56:04.272027 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:56:04.303775 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:56:04.311289 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:56:04.322752 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:56:04.348609 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:56:04.350695 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:56:04.354798 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:56:04.40697 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:56:04.40913 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:56:04.425938 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:56:04.440623 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:56:04.444982 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:56:04.459415 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:56:04.48544 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:56:09.688117 WARNING::Fitting problem for feature 50 returning NA
2025-11-27 20:56:09.716549 WARNING::Fitting problem for feature 62 returning NA
2025-11-27 20:56:09.751305 WARNING::Fitting problem for feature 74 returning NA
2025-11-27 20:56:09.759368 WARNING::Fitting problem for feature 78 returning NA
2025-11-27 20:56:09.77137 WARNING::Fitting problem for feature 84 returning NA
2025-11-27 20:56:09.798261 WARNING::Fitting problem for feature 96 returning NA
2025-11-27 20:56:09.800413 WARNING::Fitting problem for feature 97 returning NA
2025-11-27 20:56:09.805488 WARNING::Fitting problem for feature 99 returning NA
2025-11-27 20:56:09.852335 WARNING::Fitting problem for feature 114 returning NA
2025-11-27 20:56:09.854508 WARNING::Fitting problem for feature 115 returning NA
2025-11-27 20:56:09.872844 WARNING::Fitting problem for feature 123 returning NA
2025-11-27 20:56:09.887646 WARNING::Fitting problem for feature 130 returning NA
2025-11-27 20:56:09.893431 WARNING::Fitting problem for feature 132 returning NA
2025-11-27 20:56:09.914827 WARNING::Fitting problem for feature 139 returning NA
2025-11-27 20:56:09.944602 WARNING::Fitting problem for feature 150 returning NA
2025-11-27 20:56:10.07326 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_linear.rds
2025-11-27 20:56:10.116105 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_linear.rds
2025-11-27 20:56:10.154547 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/residuals_logistic.rds
2025-11-27 20:56:10.333995 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef19c6fdac/fits/fitted_logistic.rds
2025-11-27 20:56:19.145957 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-27 20:56:19.152349 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-27 20:56:19.156972 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-27 20:56:19.17491 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-27 20:56:19.181962 ERROR::Effect name not found in metadata: d
2025-11-27 20:56:19.185817 ERROR::No user formula provided
2025-11-27 20:56:19.196459 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-27 20:56:19.200748 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-27 20:56:20.399189 INFO::Writing function arguments to log file
2025-11-27 20:56:20.404392 INFO::Verifying options selected are valid
2025-11-27 20:56:21.350967 INFO::Writing function arguments to log file
2025-11-27 20:56:21.355966 INFO::Verifying options selected are valid
2025-11-27 20:56:21.3564 INFO::Determining format of input files
2025-11-27 20:56:21.356766 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-27 20:56:21.357646 INFO::Running selected normalization method: TSS
2025-11-27 20:56:21.358215 INFO::Creating output feature tables folder
2025-11-27 20:56:21.358665 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/features/data_norm.tsv
2025-11-27 20:56:21.359308 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-27 20:56:21.359639 INFO::Total samples in data: 16
2025-11-27 20:56:21.359931 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-27 20:56:21.360237 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-27 20:56:21.360941 INFO::Total filtered features: 0
2025-11-27 20:56:21.361292 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-27 20:56:21.361711 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-27 20:56:21.362028 INFO::Filtered feature names from variance filtering:
2025-11-27 20:56:21.362349 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/features/filtered_data.tsv
2025-11-27 20:56:21.362952 INFO::Running selected transform method: LOG
2025-11-27 20:56:21.363369 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/features/data_transformed.tsv
2025-11-27 20:56:21.363989 INFO::Applying z-score to standardize continuous metadata
2025-11-27 20:56:21.366093 INFO::Running the linear model component
2025-11-27 20:56:21.371857 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:21.373718 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:21.375186 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:21.377699 INFO::Counting total values for each feature
2025-11-27 20:56:21.378386 INFO::Running the logistic model component
2025-11-27 20:56:21.383488 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:21.38643 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:21.389166 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:21.392878 INFO::Counting total values for each feature
2025-11-27 20:56:21.393745 INFO::Re-running abundances for warn_prevalence
2025-11-27 20:56:21.394194 INFO::Running selected normalization method: TSS
2025-11-27 20:56:21.394801 INFO::Running selected transform method: LOG
2025-11-27 20:56:21.400681 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:21.402407 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:21.403916 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:21.433011 INFO::Creating fits folder
2025-11-27 20:56:21.433819 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/fits/residuals_linear.rds
2025-11-27 20:56:21.434409 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/fits/fitted_linear.rds
2025-11-27 20:56:21.434921 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/fits/residuals_logistic.rds
2025-11-27 20:56:21.435408 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/fits/fitted_logistic.rds
2025-11-27 20:56:21.436541 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/all_results.tsv
2025-11-27 20:56:21.437255 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//RtmpFkWC93/file68ef6b6da3bd/significant_results.tsv
2025-11-27 20:56:21.437821 INFO::Creating output figures folder
2025-11-27 20:56:21.438302 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/figures/summary_plot.pdf
2025-11-27 20:56:22.102903 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/figures
2025-11-27 20:56:22.103702 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-27 20:56:22.105854 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-27 20:56:22.34237 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/figures/summary_plot.pdf
2025-11-27 20:56:23.005943 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef6b6da3bd/figures
2025-11-27 20:56:23.006525 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-27 20:56:23.008412 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-27 20:56:23.219465 INFO::Running the linear model component
2025-11-27 20:56:23.222341 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:23.223858 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:23.225053 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:23.227335 INFO::Counting total values for each feature
2025-11-27 20:56:23.227872 INFO::Running the logistic model component
2025-11-27 20:56:23.230398 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:23.232275 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:23.233955 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:23.236567 INFO::Counting total values for each feature
2025-11-27 20:56:23.237217 INFO::Re-running abundances for warn_prevalence
2025-11-27 20:56:23.237443 INFO::Running selected normalization method: TSS
2025-11-27 20:56:23.237852 INFO::Running selected transform method: LOG
2025-11-27 20:56:23.240468 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:23.241784 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:23.242949 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:23.277022 INFO::Creating output folder
2025-11-27 20:56:23.277477 INFO::Creating output figures folder
2025-11-27 20:56:23.277922 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef773a29d4/figures/summary_plot.pdf
2025-11-27 20:56:23.906596 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef773a29d4/figures
2025-11-27 20:56:23.907187 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-27 20:56:23.908961 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-27 20:56:24.351805 INFO::Applying z-score to standardize continuous metadata
2025-11-27 20:56:24.354722 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-27 20:56:24.354993 INFO::Bypass z-score application to metadata
2025-11-27 20:56:24.355778 INFO::Bypass z-score application to metadata
2025-11-27 20:56:24.362811 INFO::Determining format of input files
2025-11-27 20:56:24.363114 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-27 20:56:24.363357 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-27 20:56:24.367402 INFO::Determining format of input files
2025-11-27 20:56:24.367766 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-27 20:56:24.368166 INFO::Input format is feature_specific_covariate samples as columns
2025-11-27 20:56:24.370729 INFO::Determining format of input files
2025-11-27 20:56:24.371012 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-27 20:56:24.371312 INFO::Input format is feature_specific_covariate samples as columns
2025-11-27 20:56:24.37177 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-27 20:56:24.371989 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-27 20:56:24.37579 INFO::Running selected transform method: LOG
2025-11-27 20:56:24.376126 INFO::Creating output feature tables folder
2025-11-27 20:56:24.376864 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef650a9a3b/features/data_transformed.tsv
2025-11-27 20:56:24.378644 INFO::Running selected transform method: LOG
2025-11-27 20:56:24.379028 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef650a9a3b/features/data_transformed.tsv
2025-11-27 20:56:24.380409 INFO::Running selected transform method: PLOG
2025-11-27 20:56:24.380936 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef650a9a3b/features/data_transformed.tsv
2025-11-27 20:56:24.381985 INFO::Running selected transform method: NONE
2025-11-27 20:56:24.382239 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef650a9a3b/features/data_transformed.tsv
2025-11-27 20:56:24.385264 INFO::Running the linear model component
2025-11-27 20:56:24.390533 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:24.392024 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:24.393226 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:24.395524 INFO::Counting total values for each feature
2025-11-27 20:56:24.396063 INFO::Running the logistic model component
2025-11-27 20:56:24.39859 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:24.400427 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:24.402125 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:24.404835 INFO::Counting total values for each feature
2025-11-27 20:56:24.405509 INFO::Re-running abundances for warn_prevalence
2025-11-27 20:56:24.405746 INFO::Running selected normalization method: TSS
2025-11-27 20:56:24.406171 INFO::Running selected transform method: LOG
2025-11-27 20:56:24.408984 INFO::Fitting model to feature number 1, a
2025-11-27 20:56:24.410716 INFO::Fitting model to feature number 2, b
2025-11-27 20:56:24.412303 INFO::Fitting model to feature number 3, c
2025-11-27 20:56:24.452757 INFO::Creating output folder
2025-11-27 20:56:24.453207 INFO::Creating fits folder
2025-11-27 20:56:24.453505 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef1b13cb50/fits/residuals_linear.rds
2025-11-27 20:56:24.453972 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef1b13cb50/fits/fitted_linear.rds
2025-11-27 20:56:24.454353 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef1b13cb50/fits/residuals_logistic.rds
2025-11-27 20:56:24.454727 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef1b13cb50/fits/fitted_logistic.rds
2025-11-27 20:56:24.455572 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpFkWC93/file68ef1b13cb50/all_results.tsv
2025-11-27 20:56:24.456143 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//RtmpFkWC93/file68ef1b13cb50/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
143.914 3.912 159.129
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.555 | 0.509 | 9.620 | |
| maaslin_check_arguments | 0.060 | 0.002 | 0.066 | |
| maaslin_check_formula | 0.063 | 0.004 | 0.069 | |
| maaslin_compute_formula | 0.064 | 0.003 | 0.075 | |
| maaslin_contrast_test | 7.430 | 0.723 | 8.799 | |
| maaslin_filter | 0.237 | 0.021 | 0.300 | |
| maaslin_fit | 5.023 | 0.600 | 6.099 | |
| maaslin_log_arguments | 0.058 | 0.003 | 0.064 | |
| maaslin_normalize | 0.134 | 0.014 | 0.158 | |
| maaslin_plot_results | 16.868 | 0.641 | 19.093 | |
| maaslin_plot_results_from_output | 16.958 | 0.700 | 18.779 | |
| maaslin_process_metadata | 0.234 | 0.015 | 0.271 | |
| maaslin_read_data | 0.055 | 0.003 | 0.063 | |
| maaslin_reorder_data | 0.054 | 0.004 | 0.059 | |
| maaslin_transform | 0.330 | 0.041 | 0.405 | |
| maaslin_write_results | 5.876 | 0.435 | 6.871 | |
| maaslin_write_results_lefse_format | 5.477 | 0.380 | 6.234 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.002 | |