William Nickols
| Snapshot Date: 2025-12-12 13:40 -0500 (Fri, 12 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 2025-12-13 11:47 -0500 (Sat, 13 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" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 1158/2332 | 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: 2025-12-12 20:57:21 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 21:02:41 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 320.2 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_from_output 17.316 0.637 18.876
maaslin_plot_results 17.065 0.638 18.794
maaslin3 8.344 0.546 9.240
maaslin_contrast_test 7.756 0.717 8.907
maaslin_write_results 6.078 0.572 7.029
maaslin_write_results_lefse_format 5.886 0.527 6.713
maaslin_fit 5.029 0.589 6.038
* 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")
2025-12-12 21:00:06.132269 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:06.170142 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:06.200662 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:06.20909 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:06.225895 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:06.256539 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:06.258921 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:06.263059 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:06.300017 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:06.302091 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:06.324941 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:06.339023 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:06.348361 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:06.362128 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:06.392481 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:00:13.615307 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:13.644327 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:13.671474 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:13.6792 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:13.691035 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:13.727754 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:13.729836 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:13.734029 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:13.771856 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:13.773958 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:13.790662 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:13.805091 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:13.809439 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:13.823452 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:13.847365 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:00:15.446 R[84859:383373542] XType: Using static font registry.
2025-12-12 21:00:23.854075 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:23.883687 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:23.913353 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:23.923258 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:23.938071 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:23.967482 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:23.969602 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:23.973835 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:24.007303 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:24.009366 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:24.026612 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:24.041486 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:24.04599 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:24.060215 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:24.089494 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:00:29.691857 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:29.721868 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:29.748155 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:29.755907 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:29.768142 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:29.796758 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:29.798821 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:29.802989 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:29.838271 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:29.840762 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:29.861826 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:29.878622 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:29.883437 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:29.900944 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:29.927243 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:00:30.025135 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/residuals_linear.rds
2025-12-12 21:00:30.059183 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/fitted_linear.rds
2025-12-12 21:00:30.096197 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/residuals_logistic.rds
2025-12-12 21:00:30.282275 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/fitted_logistic.rds
2025-12-12 21:00:40.221514 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:40.248273 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:40.276528 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:40.285691 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:40.298456 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:40.325153 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:40.327233 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:40.331478 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:40.371631 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:40.374028 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:40.392338 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:40.406117 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:40.410795 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:40.424357 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:40.455494 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:00:45.586076 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:45.613664 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:45.641209 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:45.651109 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:45.665999 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:45.692962 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:45.695166 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:45.699542 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:45.747509 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:45.750089 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:45.768303 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:45.781972 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:45.786244 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:45.801793 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:45.830175 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:00:45.921302 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/residuals_linear.rds
2025-12-12 21:00:45.96483 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/fitted_linear.rds
2025-12-12 21:00:45.999215 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/residuals_logistic.rds
2025-12-12 21:00:46.188625 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/fitted_logistic.rds
2025-12-12 21:00:55.100984 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:00:55.128623 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:00:55.156385 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:00:55.164367 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:00:55.18235 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:00:55.208514 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:00:55.210603 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:00:55.214919 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:00:55.254225 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:00:55.256933 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:00:55.28336 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:00:55.298232 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:00:55.30355 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:00:55.320236 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:00:55.350841 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:01:00.612494 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:01:00.643862 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:01:00.673854 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:01:00.68423 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:01:00.696144 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:01:00.722368 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:01:00.724943 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:01:00.729527 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:01:00.763126 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:01:00.765257 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:01:00.782118 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:01:00.799985 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:01:00.80457 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:01:00.819535 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:01:00.850989 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:01:00.934441 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/residuals_linear.rds
2025-12-12 21:01:00.97221 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/fitted_linear.rds
2025-12-12 21:01:01.006486 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/residuals_logistic.rds
2025-12-12 21:01:01.181516 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7bd53cee3/fits/fitted_logistic.rds
2025-12-12 21:01:10.023546 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:01:10.04957 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:01:10.077892 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:01:10.085821 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:01:10.098087 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:01:10.128826 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:01:10.131089 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:01:10.135587 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:01:10.175109 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:01:10.177255 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:01:10.19526 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:01:10.209959 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:01:10.214451 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:01:10.231694 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:01:10.263551 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:01:15.740956 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:01:15.771173 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:01:15.800164 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:01:15.808045 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:01:15.820595 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:01:15.847123 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:01:15.851453 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:01:15.855762 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:01:15.896358 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:01:15.898635 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:01:15.916601 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:01:15.93074 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:01:15.935341 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:01:15.950161 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:01:15.980303 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:01:25.847452 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:01:29.974148 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:01:40.512254 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:01:44.688668 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:01:44.890566 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_linear.rds
2025-12-12 21:01:44.925835 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_linear.rds
2025-12-12 21:01:44.952565 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_logistic.rds
2025-12-12 21:01:44.996952 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_logistic.rds
2025-12-12 21:01:54.584104 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:01:57.287867 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:01:57.428827 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_linear.rds
2025-12-12 21:01:57.46466 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_linear.rds
2025-12-12 21:01:57.487298 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_logistic.rds
2025-12-12 21:01:57.533656 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_logistic.rds
2025-12-12 21:02:05.69267 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:02:08.531919 WARNING::Fitting problem for feature 124 returning NA
2025-12-12 21:02:08.648323 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_linear.rds
2025-12-12 21:02:08.683526 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_linear.rds
2025-12-12 21:02:08.710437 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_logistic.rds
2025-12-12 21:02:08.75159 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_logistic.rds
2025-12-12 21:02:16.746223 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:02:16.776229 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:02:16.804508 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:02:16.81294 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:02:16.827163 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:02:16.859653 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:02:16.868585 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:02:16.873193 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:02:16.908241 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:02:16.910379 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:02:16.927752 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:02:16.960322 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:02:16.964613 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:02:16.979227 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:02:17.00723 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:02:22.324663 WARNING::Fitting problem for feature 50 returning NA
2025-12-12 21:02:22.352518 WARNING::Fitting problem for feature 62 returning NA
2025-12-12 21:02:22.382655 WARNING::Fitting problem for feature 74 returning NA
2025-12-12 21:02:22.391081 WARNING::Fitting problem for feature 78 returning NA
2025-12-12 21:02:22.403548 WARNING::Fitting problem for feature 84 returning NA
2025-12-12 21:02:22.430806 WARNING::Fitting problem for feature 96 returning NA
2025-12-12 21:02:22.432995 WARNING::Fitting problem for feature 97 returning NA
2025-12-12 21:02:22.437767 WARNING::Fitting problem for feature 99 returning NA
2025-12-12 21:02:22.477944 WARNING::Fitting problem for feature 114 returning NA
2025-12-12 21:02:22.480584 WARNING::Fitting problem for feature 115 returning NA
2025-12-12 21:02:22.504734 WARNING::Fitting problem for feature 123 returning NA
2025-12-12 21:02:22.521944 WARNING::Fitting problem for feature 130 returning NA
2025-12-12 21:02:22.526919 WARNING::Fitting problem for feature 132 returning NA
2025-12-12 21:02:22.543138 WARNING::Fitting problem for feature 139 returning NA
2025-12-12 21:02:22.570136 WARNING::Fitting problem for feature 150 returning NA
2025-12-12 21:02:22.691735 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_linear.rds
2025-12-12 21:02:22.726231 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_linear.rds
2025-12-12 21:02:22.763933 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/residuals_logistic.rds
2025-12-12 21:02:22.954005 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b1887fb60/fits/fitted_logistic.rds
2025-12-12 21:02:31.506174 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-12 21:02:31.511787 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-12 21:02:31.515704 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-12 21:02:31.536118 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-12 21:02:31.542008 ERROR::Effect name not found in metadata: d
2025-12-12 21:02:31.545581 ERROR::No user formula provided
2025-12-12 21:02:31.556353 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-12 21:02:31.560603 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-12 21:02:32.793211 INFO::Writing function arguments to log file
2025-12-12 21:02:32.798586 INFO::Verifying options selected are valid
2025-12-12 21:02:33.74217 INFO::Writing function arguments to log file
2025-12-12 21:02:33.747279 INFO::Verifying options selected are valid
2025-12-12 21:02:33.747671 INFO::Determining format of input files
2025-12-12 21:02:33.747989 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-12 21:02:33.748827 INFO::Running selected normalization method: TSS
2025-12-12 21:02:33.749402 INFO::Creating output feature tables folder
2025-12-12 21:02:33.749837 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/features/data_norm.tsv
2025-12-12 21:02:33.750552 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-12 21:02:33.750901 INFO::Total samples in data: 16
2025-12-12 21:02:33.751207 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-12 21:02:33.751518 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-12 21:02:33.752241 INFO::Total filtered features: 0
2025-12-12 21:02:33.752605 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-12 21:02:33.753043 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-12 21:02:33.753377 INFO::Filtered feature names from variance filtering:
2025-12-12 21:02:33.753699 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/features/filtered_data.tsv
2025-12-12 21:02:33.754325 INFO::Running selected transform method: LOG
2025-12-12 21:02:33.75476 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/features/data_transformed.tsv
2025-12-12 21:02:33.75544 INFO::Applying z-score to standardize continuous metadata
2025-12-12 21:02:33.757471 INFO::Running the linear model component
2025-12-12 21:02:33.762965 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:33.764703 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:33.766173 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:33.768601 INFO::Counting total values for each feature
2025-12-12 21:02:33.769304 INFO::Running the logistic model component
2025-12-12 21:02:33.774738 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:33.777014 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:33.778996 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:33.782241 INFO::Counting total values for each feature
2025-12-12 21:02:33.783128 INFO::Re-running abundances for warn_prevalence
2025-12-12 21:02:33.783524 INFO::Running selected normalization method: TSS
2025-12-12 21:02:33.784057 INFO::Running selected transform method: LOG
2025-12-12 21:02:33.790076 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:33.791915 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:33.793519 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:33.824033 INFO::Creating fits folder
2025-12-12 21:02:33.827422 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/fits/residuals_linear.rds
2025-12-12 21:02:33.828251 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/fits/fitted_linear.rds
2025-12-12 21:02:33.828993 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/fits/residuals_logistic.rds
2025-12-12 21:02:33.829558 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/fits/fitted_logistic.rds
2025-12-12 21:02:33.83065 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/all_results.tsv
2025-12-12 21:02:33.831872 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//Rtmp2cdo4C/file14b7b4f87623a/significant_results.tsv
2025-12-12 21:02:33.832549 INFO::Creating output figures folder
2025-12-12 21:02:33.833095 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/figures/summary_plot.pdf
2025-12-12 21:02:34.488475 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/figures
2025-12-12 21:02:34.489599 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-12 21:02:34.49667 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-12 21:02:34.724006 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/figures/summary_plot.pdf
2025-12-12 21:02:35.370517 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b4f87623a/figures
2025-12-12 21:02:35.37128 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-12 21:02:35.373179 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-12 21:02:35.593743 INFO::Running the linear model component
2025-12-12 21:02:35.59755 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:35.599022 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:35.60026 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:35.602683 INFO::Counting total values for each feature
2025-12-12 21:02:35.603259 INFO::Running the logistic model component
2025-12-12 21:02:35.605856 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:35.607787 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:35.609491 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:35.614371 INFO::Counting total values for each feature
2025-12-12 21:02:35.61518 INFO::Re-running abundances for warn_prevalence
2025-12-12 21:02:35.615438 INFO::Running selected normalization method: TSS
2025-12-12 21:02:35.61591 INFO::Running selected transform method: LOG
2025-12-12 21:02:35.618731 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:35.620228 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:35.621481 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:35.658038 INFO::Creating output folder
2025-12-12 21:02:35.658573 INFO::Creating output figures folder
2025-12-12 21:02:35.662316 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b134ee3c9/figures/summary_plot.pdf
2025-12-12 21:02:36.310667 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b134ee3c9/figures
2025-12-12 21:02:36.311335 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-12 21:02:36.313198 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-12 21:02:36.750333 INFO::Applying z-score to standardize continuous metadata
2025-12-12 21:02:36.754116 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-12 21:02:36.754428 INFO::Bypass z-score application to metadata
2025-12-12 21:02:36.755266 INFO::Bypass z-score application to metadata
2025-12-12 21:02:36.762879 INFO::Determining format of input files
2025-12-12 21:02:36.763232 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-12 21:02:36.763506 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-12 21:02:36.76589 INFO::Determining format of input files
2025-12-12 21:02:36.766242 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-12 21:02:36.766647 INFO::Input format is feature_specific_covariate samples as columns
2025-12-12 21:02:36.769319 INFO::Determining format of input files
2025-12-12 21:02:36.76962 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-12 21:02:36.769935 INFO::Input format is feature_specific_covariate samples as columns
2025-12-12 21:02:36.770388 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-12 21:02:36.770606 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-12 21:02:36.774613 INFO::Running selected transform method: LOG
2025-12-12 21:02:36.775013 INFO::Creating output feature tables folder
2025-12-12 21:02:36.775412 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b22300114/features/data_transformed.tsv
2025-12-12 21:02:36.776855 INFO::Running selected transform method: LOG
2025-12-12 21:02:36.777197 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b22300114/features/data_transformed.tsv
2025-12-12 21:02:36.77847 INFO::Running selected transform method: PLOG
2025-12-12 21:02:36.779011 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b22300114/features/data_transformed.tsv
2025-12-12 21:02:36.780027 INFO::Running selected transform method: NONE
2025-12-12 21:02:36.78029 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b22300114/features/data_transformed.tsv
2025-12-12 21:02:36.783544 INFO::Running the linear model component
2025-12-12 21:02:36.786285 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:36.787825 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:36.78905 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:36.791473 INFO::Counting total values for each feature
2025-12-12 21:02:36.792038 INFO::Running the logistic model component
2025-12-12 21:02:36.79467 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:36.796742 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:36.798503 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:36.801262 INFO::Counting total values for each feature
2025-12-12 21:02:36.801964 INFO::Re-running abundances for warn_prevalence
2025-12-12 21:02:36.802212 INFO::Running selected normalization method: TSS
2025-12-12 21:02:36.802651 INFO::Running selected transform method: LOG
2025-12-12 21:02:36.805445 INFO::Fitting model to feature number 1, a
2025-12-12 21:02:36.806858 INFO::Fitting model to feature number 2, b
2025-12-12 21:02:36.808045 INFO::Fitting model to feature number 3, c
2025-12-12 21:02:36.835025 INFO::Creating output folder
2025-12-12 21:02:36.835448 INFO::Creating fits folder
2025-12-12 21:02:36.835745 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b7d96d994/fits/residuals_linear.rds
2025-12-12 21:02:36.836201 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b7d96d994/fits/fitted_linear.rds
2025-12-12 21:02:36.836583 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b7d96d994/fits/residuals_logistic.rds
2025-12-12 21:02:36.836975 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b7d96d994/fits/fitted_logistic.rds
2025-12-12 21:02:36.837846 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp2cdo4C/file14b7b7d96d994/all_results.tsv
2025-12-12 21:02:36.838433 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//Rtmp2cdo4C/file14b7b7d96d994/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.260 4.517 155.942
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.344 | 0.546 | 9.240 | |
| maaslin_check_arguments | 0.066 | 0.002 | 0.071 | |
| maaslin_check_formula | 0.065 | 0.004 | 0.075 | |
| maaslin_compute_formula | 0.075 | 0.005 | 0.080 | |
| maaslin_contrast_test | 7.756 | 0.717 | 8.907 | |
| maaslin_filter | 0.227 | 0.019 | 0.254 | |
| maaslin_fit | 5.029 | 0.589 | 6.038 | |
| maaslin_log_arguments | 0.057 | 0.003 | 0.061 | |
| maaslin_normalize | 0.127 | 0.012 | 0.162 | |
| maaslin_plot_results | 17.065 | 0.638 | 18.794 | |
| maaslin_plot_results_from_output | 17.316 | 0.637 | 18.876 | |
| maaslin_process_metadata | 0.242 | 0.021 | 0.282 | |
| maaslin_read_data | 0.055 | 0.003 | 0.059 | |
| maaslin_reorder_data | 0.054 | 0.002 | 0.068 | |
| maaslin_transform | 0.274 | 0.023 | 0.335 | |
| maaslin_write_results | 6.078 | 0.572 | 7.029 | |
| maaslin_write_results_lefse_format | 5.886 | 0.527 | 6.713 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.002 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |