William Nickols
| Snapshot Date: 2025-11-06 13:45 -0500 (Thu, 06 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-07 12:01 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | 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: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-11-06 20:30:06 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 20:34:57 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 290.7 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 16.380 0.585 17.059
maaslin_plot_results 16.051 0.673 16.791
maaslin3 8.291 0.504 8.817
maaslin_contrast_test 7.163 0.642 7.850
maaslin_write_results 5.593 0.493 6.124
maaslin_write_results_lefse_format 5.370 0.512 5.927
maaslin_fit 4.988 0.576 5.576
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.2.0’ ** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
2025-11-06 20:32:33.510559 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:32:33.861362 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:32:33.890418 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:32:33.898294 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:32:33.910614 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:32:33.941714 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:32:33.943729 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:32:33.947653 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:32:33.978709 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:32:33.980624 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:32:33.99703 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:32:34.010916 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:32:34.019555 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:32:34.032503 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:32:34.055023 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:32:40.556336 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:32:40.583421 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:32:40.609507 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:32:40.617215 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:32:40.629282 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:32:40.658369 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:32:40.660441 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:32:40.664517 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:32:40.708999 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:32:40.711083 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:32:40.72738 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:32:40.740597 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:32:40.744732 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:32:40.758192 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:32:40.781806 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:32:42.223 R[34456:651157747] XType: Using static font registry.
2025-11-06 20:32:49.705414 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:32:49.730977 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:32:49.756079 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:32:49.763715 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:32:49.775826 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:32:49.803203 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:32:49.805334 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:32:49.809574 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:32:50.244805 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:32:50.24692 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:32:50.263821 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:32:50.277876 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:32:50.282339 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:32:50.297645 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:32:50.321308 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:32:55.705031 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:32:55.73197 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:32:55.758579 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:32:55.766165 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:32:55.777633 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:32:55.80328 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:32:55.805288 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:32:55.809358 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:32:55.841727 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:32:55.843633 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:32:55.861106 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:32:55.875182 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:32:55.87938 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:32:55.893099 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:32:55.916667 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:32:55.997895 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/residuals_linear.rds
2025-11-06 20:32:56.030164 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/fitted_linear.rds
2025-11-06 20:32:56.063736 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/residuals_logistic.rds
2025-11-06 20:32:56.232424 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/fitted_logistic.rds
2025-11-06 20:33:04.410037 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:33:04.438662 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:33:04.469079 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:33:04.477752 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:33:04.491714 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:33:04.525166 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:33:04.527271 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:33:04.531325 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:33:04.564096 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:33:04.56609 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:33:04.583542 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:33:04.597443 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:33:04.601656 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:33:04.615698 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:33:04.640091 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:33:10.19561 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:33:10.223285 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:33:10.250194 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:33:10.258299 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:33:10.270554 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:33:10.298172 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:33:10.300301 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:33:10.304601 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:33:10.339715 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:33:10.341864 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:33:10.360012 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:33:10.374971 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:33:10.379896 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:33:10.394715 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:33:10.418264 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:33:10.492499 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/residuals_linear.rds
2025-11-06 20:33:10.52495 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/fitted_linear.rds
2025-11-06 20:33:10.559093 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/residuals_logistic.rds
2025-11-06 20:33:10.725858 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/fitted_logistic.rds
2025-11-06 20:33:18.921787 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:33:18.948214 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:33:18.974834 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:33:18.982799 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:33:18.994957 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:33:19.022692 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:33:19.024723 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:33:19.029003 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:33:19.064207 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:33:19.066348 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:33:19.085506 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:33:19.100336 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:33:19.104965 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:33:19.119743 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:33:19.143715 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:33:24.366003 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:33:24.393007 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:33:24.420417 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:33:24.428616 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:33:24.441408 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:33:24.469871 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:33:24.472058 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:33:24.476866 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:33:24.51235 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:33:24.514651 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:33:24.533455 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:33:24.548638 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:33:24.553636 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:33:24.569204 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:33:24.593878 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:33:24.688577 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/residuals_linear.rds
2025-11-06 20:33:24.720699 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/fitted_linear.rds
2025-11-06 20:33:24.753915 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/residuals_logistic.rds
2025-11-06 20:33:24.921614 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869834135709/fits/fitted_logistic.rds
2025-11-06 20:33:32.999491 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:33:33.027817 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:33:33.055116 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:33:33.063124 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:33:33.075441 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:33:33.102613 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:33:33.104711 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:33:33.108861 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:33:33.14092 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:33:33.143006 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:33:33.159581 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:33:33.173408 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:33:33.177671 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:33:33.191208 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:33:33.216233 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:33:38.369282 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:33:38.395987 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:33:38.422387 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:33:38.430604 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:33:38.44279 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:33:38.491241 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:33:38.493259 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:33:38.497286 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:33:38.529169 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:33:38.531157 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:33:38.547629 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:33:38.561082 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:33:38.565561 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:33:38.579556 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:33:38.603114 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:33:47.516517 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:33:51.634669 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:01.051112 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:04.94422 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:05.128917 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_linear.rds
2025-11-06 20:34:05.161719 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_linear.rds
2025-11-06 20:34:05.184042 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_logistic.rds
2025-11-06 20:34:05.225688 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_logistic.rds
2025-11-06 20:34:13.884637 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:16.641218 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:16.73875 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_linear.rds
2025-11-06 20:34:16.771662 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_linear.rds
2025-11-06 20:34:16.793627 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_logistic.rds
2025-11-06 20:34:16.83473 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_logistic.rds
2025-11-06 20:34:24.09635 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:26.250907 WARNING::Fitting problem for feature 124 returning NA
2025-11-06 20:34:26.348933 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_linear.rds
2025-11-06 20:34:26.381829 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_linear.rds
2025-11-06 20:34:26.40396 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_logistic.rds
2025-11-06 20:34:26.443495 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_logistic.rds
2025-11-06 20:34:34.157778 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:34:34.183778 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:34:34.209393 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:34:34.216836 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:34:34.228542 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:34:34.25444 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:34:34.256451 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:34:34.260491 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:34:34.292397 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:34:34.296898 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:34:34.313768 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:34:34.327031 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:34:34.331102 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:34:34.34453 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:34:34.368419 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:34:39.067709 WARNING::Fitting problem for feature 50 returning NA
2025-11-06 20:34:39.095061 WARNING::Fitting problem for feature 62 returning NA
2025-11-06 20:34:39.122094 WARNING::Fitting problem for feature 74 returning NA
2025-11-06 20:34:39.130338 WARNING::Fitting problem for feature 78 returning NA
2025-11-06 20:34:39.708579 WARNING::Fitting problem for feature 84 returning NA
2025-11-06 20:34:39.736424 WARNING::Fitting problem for feature 96 returning NA
2025-11-06 20:34:39.73862 WARNING::Fitting problem for feature 97 returning NA
2025-11-06 20:34:39.742978 WARNING::Fitting problem for feature 99 returning NA
2025-11-06 20:34:39.778248 WARNING::Fitting problem for feature 114 returning NA
2025-11-06 20:34:39.780399 WARNING::Fitting problem for feature 115 returning NA
2025-11-06 20:34:39.797694 WARNING::Fitting problem for feature 123 returning NA
2025-11-06 20:34:39.81185 WARNING::Fitting problem for feature 130 returning NA
2025-11-06 20:34:39.816189 WARNING::Fitting problem for feature 132 returning NA
2025-11-06 20:34:39.830284 WARNING::Fitting problem for feature 139 returning NA
2025-11-06 20:34:39.854687 WARNING::Fitting problem for feature 150 returning NA
2025-11-06 20:34:39.943013 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_linear.rds
2025-11-06 20:34:39.975298 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_linear.rds
2025-11-06 20:34:40.009108 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/residuals_logistic.rds
2025-11-06 20:34:40.185711 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86981638988b/fits/fitted_logistic.rds
2025-11-06 20:34:48.496103 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-06 20:34:48.503112 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-06 20:34:48.507867 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-06 20:34:48.528288 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-06 20:34:48.535304 ERROR::Effect name not found in metadata: d
2025-11-06 20:34:48.539987 ERROR::No user formula provided
2025-11-06 20:34:48.551508 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-06 20:34:48.556434 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-06 20:34:49.576121 INFO::Writing function arguments to log file
2025-11-06 20:34:49.582026 INFO::Verifying options selected are valid
2025-11-06 20:34:50.460196 INFO::Writing function arguments to log file
2025-11-06 20:34:50.464613 INFO::Verifying options selected are valid
2025-11-06 20:34:50.465023 INFO::Determining format of input files
2025-11-06 20:34:50.465353 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-06 20:34:50.466144 INFO::Running selected normalization method: TSS
2025-11-06 20:34:50.466688 INFO::Creating output feature tables folder
2025-11-06 20:34:50.467094 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/features/data_norm.tsv
2025-11-06 20:34:50.46768 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-06 20:34:50.46801 INFO::Total samples in data: 16
2025-11-06 20:34:50.468295 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-06 20:34:50.468585 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-06 20:34:50.46922 INFO::Total filtered features: 0
2025-11-06 20:34:50.469558 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-06 20:34:50.469931 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-06 20:34:50.470232 INFO::Filtered feature names from variance filtering:
2025-11-06 20:34:50.470514 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/features/filtered_data.tsv
2025-11-06 20:34:50.471072 INFO::Running selected transform method: LOG
2025-11-06 20:34:50.471478 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/features/data_transformed.tsv
2025-11-06 20:34:50.472058 INFO::Applying z-score to standardize continuous metadata
2025-11-06 20:34:50.473914 INFO::Running the linear model component
2025-11-06 20:34:50.4788 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:50.480385 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:50.481788 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:50.484283 INFO::Counting total values for each feature
2025-11-06 20:34:50.484947 INFO::Running the logistic model component
2025-11-06 20:34:50.489966 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:50.492123 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:50.494055 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:50.497058 INFO::Counting total values for each feature
2025-11-06 20:34:50.497914 INFO::Re-running abundances for warn_prevalence
2025-11-06 20:34:50.498346 INFO::Running selected normalization method: TSS
2025-11-06 20:34:50.498886 INFO::Running selected transform method: LOG
2025-11-06 20:34:50.503991 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:50.50551 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:50.506793 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:50.533734 INFO::Creating fits folder
2025-11-06 20:34:50.534312 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/fits/residuals_linear.rds
2025-11-06 20:34:50.534815 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/fits/fitted_linear.rds
2025-11-06 20:34:50.53525 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/fits/residuals_logistic.rds
2025-11-06 20:34:50.535694 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/fits/fitted_logistic.rds
2025-11-06 20:34:50.536652 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/all_results.tsv
2025-11-06 20:34:50.537311 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//RtmpXdcvQw/file869841daaf84/significant_results.tsv
2025-11-06 20:34:50.537804 INFO::Creating output figures folder
2025-11-06 20:34:50.538266 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/figures/summary_plot.pdf
2025-11-06 20:34:51.119113 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/figures
2025-11-06 20:34:51.119934 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-06 20:34:51.121837 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-06 20:34:51.31606 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/figures/summary_plot.pdf
2025-11-06 20:34:51.904644 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869841daaf84/figures
2025-11-06 20:34:51.905204 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-06 20:34:51.906937 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-06 20:34:52.100528 INFO::Running the linear model component
2025-11-06 20:34:52.103336 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:52.104791 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:52.10598 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:52.108293 INFO::Counting total values for each feature
2025-11-06 20:34:52.10883 INFO::Running the logistic model component
2025-11-06 20:34:52.111298 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:52.113152 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:52.11486 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:52.117475 INFO::Counting total values for each feature
2025-11-06 20:34:52.118113 INFO::Re-running abundances for warn_prevalence
2025-11-06 20:34:52.118347 INFO::Running selected normalization method: TSS
2025-11-06 20:34:52.118756 INFO::Running selected transform method: LOG
2025-11-06 20:34:52.121324 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:52.122564 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:52.12371 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:52.14967 INFO::Creating output folder
2025-11-06 20:34:52.150099 INFO::Creating output figures folder
2025-11-06 20:34:52.150533 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86986969fa1b/figures/summary_plot.pdf
2025-11-06 20:34:52.750764 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file86986969fa1b/figures
2025-11-06 20:34:52.751401 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-06 20:34:52.753338 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-06 20:34:53.137623 INFO::Applying z-score to standardize continuous metadata
2025-11-06 20:34:53.140389 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-06 20:34:53.140659 INFO::Bypass z-score application to metadata
2025-11-06 20:34:53.141416 INFO::Bypass z-score application to metadata
2025-11-06 20:34:53.147729 INFO::Determining format of input files
2025-11-06 20:34:53.148026 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-06 20:34:53.148272 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-06 20:34:53.150355 INFO::Determining format of input files
2025-11-06 20:34:53.150661 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-06 20:34:53.151025 INFO::Input format is feature_specific_covariate samples as columns
2025-11-06 20:34:53.15333 INFO::Determining format of input files
2025-11-06 20:34:53.153613 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-06 20:34:53.153908 INFO::Input format is feature_specific_covariate samples as columns
2025-11-06 20:34:53.154359 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-06 20:34:53.154573 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-06 20:34:53.157945 INFO::Running selected transform method: LOG
2025-11-06 20:34:53.158288 INFO::Creating output feature tables folder
2025-11-06 20:34:53.158639 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869847d2e454/features/data_transformed.tsv
2025-11-06 20:34:53.159915 INFO::Running selected transform method: LOG
2025-11-06 20:34:53.16032 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869847d2e454/features/data_transformed.tsv
2025-11-06 20:34:53.161612 INFO::Running selected transform method: PLOG
2025-11-06 20:34:53.162125 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869847d2e454/features/data_transformed.tsv
2025-11-06 20:34:53.163076 INFO::Running selected transform method: NONE
2025-11-06 20:34:53.163312 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file869847d2e454/features/data_transformed.tsv
2025-11-06 20:34:53.165845 INFO::Running the linear model component
2025-11-06 20:34:53.168436 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:53.16984 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:53.171075 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:53.173416 INFO::Counting total values for each feature
2025-11-06 20:34:53.173997 INFO::Running the logistic model component
2025-11-06 20:34:53.176691 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:53.178641 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:53.180544 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:53.183393 INFO::Counting total values for each feature
2025-11-06 20:34:53.184063 INFO::Re-running abundances for warn_prevalence
2025-11-06 20:34:53.184298 INFO::Running selected normalization method: TSS
2025-11-06 20:34:53.184713 INFO::Running selected transform method: LOG
2025-11-06 20:34:53.187315 INFO::Fitting model to feature number 1, a
2025-11-06 20:34:53.188564 INFO::Fitting model to feature number 2, b
2025-11-06 20:34:53.189727 INFO::Fitting model to feature number 3, c
2025-11-06 20:34:53.217877 INFO::Creating output folder
2025-11-06 20:34:53.218298 INFO::Creating fits folder
2025-11-06 20:34:53.218601 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file8698668c6ba2/fits/residuals_linear.rds
2025-11-06 20:34:53.219073 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file8698668c6ba2/fits/fitted_linear.rds
2025-11-06 20:34:53.219452 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file8698668c6ba2/fits/residuals_logistic.rds
2025-11-06 20:34:53.219864 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file8698668c6ba2/fits/fitted_logistic.rds
2025-11-06 20:34:53.220791 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXdcvQw/file8698668c6ba2/all_results.tsv
2025-11-06 20:34:53.221443 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//RtmpXdcvQw/file8698668c6ba2/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
137.455 5.674 143.918
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.291 | 0.504 | 8.817 | |
| maaslin_check_arguments | 0.062 | 0.001 | 0.063 | |
| maaslin_check_formula | 0.061 | 0.003 | 0.064 | |
| maaslin_compute_formula | 0.058 | 0.003 | 0.062 | |
| maaslin_contrast_test | 7.163 | 0.642 | 7.850 | |
| maaslin_filter | 0.218 | 0.033 | 0.253 | |
| maaslin_fit | 4.988 | 0.576 | 5.576 | |
| maaslin_log_arguments | 0.052 | 0.003 | 0.056 | |
| maaslin_normalize | 0.122 | 0.012 | 0.176 | |
| maaslin_plot_results | 16.051 | 0.673 | 16.791 | |
| maaslin_plot_results_from_output | 16.380 | 0.585 | 17.059 | |
| maaslin_process_metadata | 0.232 | 0.020 | 0.254 | |
| maaslin_read_data | 0.050 | 0.003 | 0.057 | |
| maaslin_reorder_data | 0.052 | 0.002 | 0.055 | |
| maaslin_transform | 0.285 | 0.023 | 0.309 | |
| maaslin_write_results | 5.593 | 0.493 | 6.124 | |
| maaslin_write_results_lefse_format | 5.370 | 0.512 | 5.927 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |