William Nickols
| Snapshot Date: 2025-12-08 13:40 -0500 (Mon, 08 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 2025-12-09 11:35 -0500 (Tue, 09 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1157/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the maaslin3 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: maaslin3 |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz |
| StartedAt: 2025-12-08 20:40:20 -0500 (Mon, 08 Dec 2025) |
| EndedAt: 2025-12-08 20:45:38 -0500 (Mon, 08 Dec 2025) |
| EllapsedTime: 318.0 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
###
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##############################################################################
* 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 17.387 0.627 18.946
maaslin_plot_results 16.927 0.685 18.549
maaslin3 8.238 0.510 9.084
maaslin_contrast_test 7.667 0.679 8.904
maaslin_write_results_lefse_format 6.219 0.575 7.126
maaslin_write_results 5.407 0.499 6.171
maaslin_fit 5.032 0.553 6.060
* 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")
2025-12-08 20:43:04.317268 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:04.346974 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:04.38458 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:04.393607 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:04.411631 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:04.442542 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:04.444991 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:04.449784 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:04.489778 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:04.491861 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:04.510849 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:04.525319 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:04.529531 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:04.543821 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:04.578505 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:11.580832 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:11.611615 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:11.638729 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:11.646247 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:11.658183 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:11.697424 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:11.707853 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:11.712119 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:11.757592 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:11.760076 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:11.777958 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:11.791952 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:11.796395 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:11.810926 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:11.835965 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:13.445 R[41281:323610529] XType: Using static font registry.
2025-12-08 20:43:22.145182 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:22.171963 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:22.200936 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:22.210388 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:22.223804 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:22.249559 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:22.251589 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:22.255697 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:22.29504 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:22.297193 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:22.315283 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:22.329689 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:22.334085 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:22.347911 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:22.372371 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:27.99728 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:28.024643 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:28.053274 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:28.060842 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:28.074531 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:28.102976 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:28.105128 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:28.109389 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:28.147267 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:28.149302 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:28.167466 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:28.180838 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:28.191487 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:28.206787 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:28.233567 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:28.326455 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/residuals_linear.rds
2025-12-08 20:43:28.361055 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/fitted_linear.rds
2025-12-08 20:43:28.395472 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/residuals_logistic.rds
2025-12-08 20:43:28.568951 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/fitted_logistic.rds
2025-12-08 20:43:38.683748 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:38.710648 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:38.735569 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:38.743147 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:38.755884 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:38.785557 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:38.787874 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:38.792253 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:38.825737 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:38.827739 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:38.844628 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:38.861665 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:38.865947 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:38.880894 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:38.906654 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:43.976809 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:44.004145 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:44.034573 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:44.043181 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:44.056828 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:44.083563 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:44.085644 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:44.089662 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:44.131576 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:44.133912 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:44.151907 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:44.166527 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:44.171024 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:44.191547 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:44.221504 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:44.324366 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/residuals_linear.rds
2025-12-08 20:43:44.35711 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/fitted_linear.rds
2025-12-08 20:43:44.395564 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/residuals_logistic.rds
2025-12-08 20:43:44.573506 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/fitted_logistic.rds
2025-12-08 20:43:53.372835 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:53.407381 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:53.437236 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:53.445019 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:53.45685 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:53.488716 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:53.4911 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:53.495556 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:53.52898 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:53.531063 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:53.553471 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:53.572714 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:53.57718 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:53.592017 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:53.616747 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:58.800871 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:43:58.832237 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:43:58.857597 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:43:58.865193 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:43:58.877144 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:43:58.90391 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:43:58.905875 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:43:58.91006 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:43:58.943733 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:43:58.945794 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:43:58.962886 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:43:58.976999 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:43:58.981494 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:43:58.998081 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:43:59.024313 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:43:59.1142 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/residuals_linear.rds
2025-12-08 20:43:59.148046 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/fitted_linear.rds
2025-12-08 20:43:59.181378 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/residuals_logistic.rds
2025-12-08 20:43:59.363748 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14130ee9216/fits/fitted_logistic.rds
2025-12-08 20:44:08.317382 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:44:08.346566 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:44:08.372547 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:44:08.380412 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:44:08.393808 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:44:08.425748 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:44:08.427773 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:44:08.43168 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:44:08.467107 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:44:08.469328 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:44:08.496569 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:44:08.514337 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:44:08.519081 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:44:08.542879 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:44:08.567305 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:44:14.36416 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:44:14.391216 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:44:14.422338 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:44:14.43015 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:44:14.442282 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:44:14.470272 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:44:14.472431 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:44:14.47649 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:44:14.516358 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:44:14.518451 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:44:14.536254 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:44:14.551184 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:44:14.555744 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:44:14.570525 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:44:14.598094 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:44:24.431095 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:44:28.408865 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:44:38.658889 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:44:42.683173 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:44:42.896889 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_linear.rds
2025-12-08 20:44:42.934115 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_linear.rds
2025-12-08 20:44:42.95575 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_logistic.rds
2025-12-08 20:44:42.995657 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_logistic.rds
2025-12-08 20:44:52.53497 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:44:55.280538 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:44:55.415646 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_linear.rds
2025-12-08 20:44:55.452807 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_linear.rds
2025-12-08 20:44:55.483155 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_logistic.rds
2025-12-08 20:44:55.526369 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_logistic.rds
2025-12-08 20:45:03.539307 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:45:06.401391 WARNING::Fitting problem for feature 124 returning NA
2025-12-08 20:45:06.512418 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_linear.rds
2025-12-08 20:45:06.545452 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_linear.rds
2025-12-08 20:45:06.568374 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_logistic.rds
2025-12-08 20:45:06.611412 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_logistic.rds
2025-12-08 20:45:14.240364 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:45:14.270658 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:45:14.298006 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:45:14.306556 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:45:14.320315 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:45:14.351765 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:45:14.35393 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:45:14.35821 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:45:14.392467 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:45:14.394737 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:45:14.412436 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:45:14.427114 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:45:14.431611 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:45:14.446613 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:45:14.493983 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:45:19.691188 WARNING::Fitting problem for feature 50 returning NA
2025-12-08 20:45:19.719197 WARNING::Fitting problem for feature 62 returning NA
2025-12-08 20:45:19.746727 WARNING::Fitting problem for feature 74 returning NA
2025-12-08 20:45:19.754677 WARNING::Fitting problem for feature 78 returning NA
2025-12-08 20:45:19.767265 WARNING::Fitting problem for feature 84 returning NA
2025-12-08 20:45:19.79401 WARNING::Fitting problem for feature 96 returning NA
2025-12-08 20:45:19.796188 WARNING::Fitting problem for feature 97 returning NA
2025-12-08 20:45:19.800395 WARNING::Fitting problem for feature 99 returning NA
2025-12-08 20:45:19.835658 WARNING::Fitting problem for feature 114 returning NA
2025-12-08 20:45:19.837906 WARNING::Fitting problem for feature 115 returning NA
2025-12-08 20:45:19.85972 WARNING::Fitting problem for feature 123 returning NA
2025-12-08 20:45:19.874289 WARNING::Fitting problem for feature 130 returning NA
2025-12-08 20:45:19.878783 WARNING::Fitting problem for feature 132 returning NA
2025-12-08 20:45:19.893934 WARNING::Fitting problem for feature 139 returning NA
2025-12-08 20:45:19.919997 WARNING::Fitting problem for feature 150 returning NA
2025-12-08 20:45:20.04575 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_linear.rds
2025-12-08 20:45:20.079031 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_linear.rds
2025-12-08 20:45:20.115464 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/residuals_logistic.rds
2025-12-08 20:45:20.293886 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1417f0ec555/fits/fitted_logistic.rds
2025-12-08 20:45:28.7483 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-08 20:45:28.755153 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-08 20:45:28.760215 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-08 20:45:28.779315 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-08 20:45:28.786875 ERROR::Effect name not found in metadata: d
2025-12-08 20:45:28.791676 ERROR::No user formula provided
2025-12-08 20:45:28.804972 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-08 20:45:28.809597 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-08 20:45:30.035245 INFO::Writing function arguments to log file
2025-12-08 20:45:30.041033 INFO::Verifying options selected are valid
2025-12-08 20:45:30.980053 INFO::Writing function arguments to log file
2025-12-08 20:45:30.98626 INFO::Verifying options selected are valid
2025-12-08 20:45:30.986747 INFO::Determining format of input files
2025-12-08 20:45:30.98714 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-08 20:45:30.988168 INFO::Running selected normalization method: TSS
2025-12-08 20:45:30.988835 INFO::Creating output feature tables folder
2025-12-08 20:45:30.989331 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/features/data_norm.tsv
2025-12-08 20:45:30.990018 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-08 20:45:30.990347 INFO::Total samples in data: 16
2025-12-08 20:45:30.99065 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-08 20:45:30.990943 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-08 20:45:30.99162 INFO::Total filtered features: 0
2025-12-08 20:45:30.991968 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-08 20:45:30.992376 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-08 20:45:30.992692 INFO::Filtered feature names from variance filtering:
2025-12-08 20:45:30.992996 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/features/filtered_data.tsv
2025-12-08 20:45:30.993568 INFO::Running selected transform method: LOG
2025-12-08 20:45:30.993968 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/features/data_transformed.tsv
2025-12-08 20:45:30.994619 INFO::Applying z-score to standardize continuous metadata
2025-12-08 20:45:30.996626 INFO::Running the linear model component
2025-12-08 20:45:31.002285 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:31.003928 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:31.005864 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:31.00832 INFO::Counting total values for each feature
2025-12-08 20:45:31.008998 INFO::Running the logistic model component
2025-12-08 20:45:31.014452 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:31.01663 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:31.018543 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:31.022499 INFO::Counting total values for each feature
2025-12-08 20:45:31.023369 INFO::Re-running abundances for warn_prevalence
2025-12-08 20:45:31.0239 INFO::Running selected normalization method: TSS
2025-12-08 20:45:31.024432 INFO::Running selected transform method: LOG
2025-12-08 20:45:31.029612 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:31.031165 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:31.032513 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:31.064129 INFO::Creating fits folder
2025-12-08 20:45:31.064832 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/fits/residuals_linear.rds
2025-12-08 20:45:31.065443 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/fits/fitted_linear.rds
2025-12-08 20:45:31.066037 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/fits/residuals_logistic.rds
2025-12-08 20:45:31.066607 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/fits/fitted_logistic.rds
2025-12-08 20:45:31.067788 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/all_results.tsv
2025-12-08 20:45:31.068644 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//RtmpsNWLCS/filea1412b1691c9/significant_results.tsv
2025-12-08 20:45:31.069293 INFO::Creating output figures folder
2025-12-08 20:45:31.069811 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/figures/summary_plot.pdf
2025-12-08 20:45:31.724175 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/figures
2025-12-08 20:45:31.724999 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-08 20:45:31.727128 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-08 20:45:31.94704 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/figures/summary_plot.pdf
2025-12-08 20:45:32.602317 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1412b1691c9/figures
2025-12-08 20:45:32.602941 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-08 20:45:32.604762 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-08 20:45:32.831014 INFO::Running the linear model component
2025-12-08 20:45:32.833984 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:32.835468 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:32.836767 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:32.839103 INFO::Counting total values for each feature
2025-12-08 20:45:32.83967 INFO::Running the logistic model component
2025-12-08 20:45:32.842405 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:32.84455 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:32.846517 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:32.849643 INFO::Counting total values for each feature
2025-12-08 20:45:32.850384 INFO::Re-running abundances for warn_prevalence
2025-12-08 20:45:32.850657 INFO::Running selected normalization method: TSS
2025-12-08 20:45:32.851146 INFO::Running selected transform method: LOG
2025-12-08 20:45:32.853919 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:32.855244 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:32.856399 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:32.884375 INFO::Creating output folder
2025-12-08 20:45:32.884835 INFO::Creating output figures folder
2025-12-08 20:45:32.885268 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1416752612b/figures/summary_plot.pdf
2025-12-08 20:45:33.56615 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea1416752612b/figures
2025-12-08 20:45:33.566835 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-08 20:45:33.569942 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-08 20:45:34.005258 INFO::Applying z-score to standardize continuous metadata
2025-12-08 20:45:34.007976 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-08 20:45:34.008261 INFO::Bypass z-score application to metadata
2025-12-08 20:45:34.009043 INFO::Bypass z-score application to metadata
2025-12-08 20:45:34.016219 INFO::Determining format of input files
2025-12-08 20:45:34.016558 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-08 20:45:34.016833 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-08 20:45:34.019286 INFO::Determining format of input files
2025-12-08 20:45:34.019627 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-08 20:45:34.02002 INFO::Input format is feature_specific_covariate samples as columns
2025-12-08 20:45:34.022563 INFO::Determining format of input files
2025-12-08 20:45:34.022857 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-08 20:45:34.023162 INFO::Input format is feature_specific_covariate samples as columns
2025-12-08 20:45:34.023619 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-08 20:45:34.023854 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-08 20:45:34.027853 INFO::Running selected transform method: LOG
2025-12-08 20:45:34.028212 INFO::Creating output feature tables folder
2025-12-08 20:45:34.028609 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14151ec4da0/features/data_transformed.tsv
2025-12-08 20:45:34.029997 INFO::Running selected transform method: LOG
2025-12-08 20:45:34.030325 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14151ec4da0/features/data_transformed.tsv
2025-12-08 20:45:34.031716 INFO::Running selected transform method: PLOG
2025-12-08 20:45:34.032345 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14151ec4da0/features/data_transformed.tsv
2025-12-08 20:45:34.033493 INFO::Running selected transform method: NONE
2025-12-08 20:45:34.033806 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14151ec4da0/features/data_transformed.tsv
2025-12-08 20:45:34.037401 INFO::Running the linear model component
2025-12-08 20:45:34.040797 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:34.042587 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:34.04409 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:34.046942 INFO::Counting total values for each feature
2025-12-08 20:45:34.047606 INFO::Running the logistic model component
2025-12-08 20:45:34.050454 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:34.052646 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:34.054603 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:34.057721 INFO::Counting total values for each feature
2025-12-08 20:45:34.0585 INFO::Re-running abundances for warn_prevalence
2025-12-08 20:45:34.05878 INFO::Running selected normalization method: TSS
2025-12-08 20:45:34.059268 INFO::Running selected transform method: LOG
2025-12-08 20:45:34.062052 INFO::Fitting model to feature number 1, a
2025-12-08 20:45:34.06337 INFO::Fitting model to feature number 2, b
2025-12-08 20:45:34.064698 INFO::Fitting model to feature number 3, c
2025-12-08 20:45:34.098504 INFO::Creating output folder
2025-12-08 20:45:34.098943 INFO::Creating fits folder
2025-12-08 20:45:34.099246 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14170dc6d64/fits/residuals_linear.rds
2025-12-08 20:45:34.09982 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14170dc6d64/fits/fitted_linear.rds
2025-12-08 20:45:34.100269 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14170dc6d64/fits/residuals_logistic.rds
2025-12-08 20:45:34.100672 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14170dc6d64/fits/fitted_logistic.rds
2025-12-08 20:45:34.101596 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsNWLCS/filea14170dc6d64/all_results.tsv
2025-12-08 20:45:34.104461 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//RtmpsNWLCS/filea14170dc6d64/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.766 4.471 155.067
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.238 | 0.510 | 9.084 | |
| maaslin_check_arguments | 0.068 | 0.002 | 0.080 | |
| maaslin_check_formula | 0.063 | 0.004 | 0.074 | |
| maaslin_compute_formula | 0.069 | 0.004 | 0.074 | |
| maaslin_contrast_test | 7.667 | 0.679 | 8.904 | |
| maaslin_filter | 0.238 | 0.026 | 0.284 | |
| maaslin_fit | 5.032 | 0.553 | 6.060 | |
| maaslin_log_arguments | 0.061 | 0.003 | 0.066 | |
| maaslin_normalize | 0.131 | 0.011 | 0.153 | |
| maaslin_plot_results | 16.927 | 0.685 | 18.549 | |
| maaslin_plot_results_from_output | 17.387 | 0.627 | 18.946 | |
| maaslin_process_metadata | 0.247 | 0.023 | 0.284 | |
| maaslin_read_data | 0.058 | 0.003 | 0.061 | |
| maaslin_reorder_data | 0.057 | 0.004 | 0.070 | |
| maaslin_transform | 0.286 | 0.033 | 0.334 | |
| maaslin_write_results | 5.407 | 0.499 | 6.171 | |
| maaslin_write_results_lefse_format | 6.219 | 0.575 | 7.126 | |
| preprocess_dna_mtx | 0.001 | 0.001 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.002 | |