William Nickols
| Snapshot Date: 2025-12-16 13:40 -0500 (Tue, 16 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 2025-12-17 11:35 -0500 (Wed, 17 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" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4589 |
| 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: 2025-12-16 20:32:22 -0500 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 20:37:39 -0500 (Tue, 16 Dec 2025) |
| EllapsedTime: 317.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maaslin_plot_results_from_output 17.056 0.792 18.526
maaslin_plot_results 16.962 0.675 18.441
maaslin3 8.349 0.549 9.126
maaslin_contrast_test 7.445 0.684 8.562
maaslin_write_results 5.710 0.591 6.687
maaslin_write_results_lefse_format 5.508 0.400 6.189
maaslin_fit 5.152 0.549 5.962
* 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")
2025-12-16 20:35:03.881851 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:03.916957 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:03.946586 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:03.954665 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:03.974034 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:04.002495 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:04.004636 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:04.00943 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:04.049373 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:04.05147 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:04.070955 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:04.086396 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:04.091664 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:04.105933 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:04.135951 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:11.453778 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:11.482292 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:11.513918 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:11.522204 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:11.534416 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:11.578599 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:11.580567 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:11.584412 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:11.623674 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:11.625697 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:11.642802 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:11.657918 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:11.662398 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:11.678169 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:11.71029 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:13.350 R[66394:424896661] XType: Using static font registry.
2025-12-16 20:35:21.765801 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:21.796593 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:21.826461 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:21.83555 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:21.847364 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:21.876026 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:21.878553 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:21.883474 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:21.922792 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:21.924925 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:21.943802 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:21.958978 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:21.964029 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:21.980503 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:22.005058 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:27.638416 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:27.667471 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:27.697314 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:27.705954 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:27.71856 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:27.748102 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:27.750746 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:27.755984 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:27.794536 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:27.796674 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:27.814503 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:27.828895 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:27.833992 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:27.850286 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:27.881772 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:27.985183 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/residuals_linear.rds
2025-12-16 20:35:28.024908 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/fitted_linear.rds
2025-12-16 20:35:28.059911 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/residuals_logistic.rds
2025-12-16 20:35:28.237622 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/fitted_logistic.rds
2025-12-16 20:35:38.110137 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:38.140502 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:38.174885 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:38.182463 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:38.194274 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:38.227396 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:38.229568 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:38.234598 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:38.269896 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:38.272103 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:38.298855 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:38.317157 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:38.321921 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:38.336736 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:38.363434 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:43.286817 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:43.31449 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:43.340153 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:43.34795 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:43.360773 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:43.391457 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:43.393546 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:43.397424 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:43.429802 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:43.431841 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:43.448881 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:43.462406 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:43.467085 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:43.481056 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:43.508213 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:43.59455 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/residuals_linear.rds
2025-12-16 20:35:43.628289 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/fitted_linear.rds
2025-12-16 20:35:43.67039 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/residuals_logistic.rds
2025-12-16 20:35:43.85352 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/fitted_logistic.rds
2025-12-16 20:35:52.658462 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:52.697582 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:52.724929 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:52.733185 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:52.745811 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:52.777034 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:52.779125 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:52.783207 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:52.816682 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:52.819199 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:52.845906 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:52.861022 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:52.865191 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:52.878457 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:52.901718 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:58.143095 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:35:58.169915 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:35:58.196548 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:35:58.204476 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:35:58.218688 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:35:58.25565 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:35:58.257763 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:35:58.262194 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:35:58.298621 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:35:58.300743 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:35:58.318937 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:35:58.338674 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:35:58.345154 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:35:58.362048 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:35:58.392127 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:35:58.490169 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/residuals_linear.rds
2025-12-16 20:35:58.539153 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/fitted_linear.rds
2025-12-16 20:35:58.580307 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/residuals_logistic.rds
2025-12-16 20:35:58.784727 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a103ca842/fits/fitted_logistic.rds
2025-12-16 20:36:07.834523 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:36:07.865079 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:36:07.895785 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:36:07.904269 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:36:07.917151 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:36:07.945862 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:36:07.948109 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:36:07.952418 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:36:07.994463 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:36:07.996811 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:36:08.016508 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:36:08.031973 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:36:08.036613 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:36:08.052657 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:36:08.08109 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:36:13.445267 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:36:13.472008 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:36:13.498528 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:36:13.506977 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:36:13.521816 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:36:13.549721 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:36:13.551747 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:36:13.555887 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:36:13.589583 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:36:13.594137 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:36:13.614821 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:36:13.629058 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:36:13.633736 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:36:13.650563 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:36:13.680421 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:36:23.441197 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:36:27.557585 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:36:37.985476 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:36:42.062844 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:36:42.290746 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_linear.rds
2025-12-16 20:36:42.324692 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_linear.rds
2025-12-16 20:36:42.348914 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_logistic.rds
2025-12-16 20:36:42.392627 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_logistic.rds
2025-12-16 20:36:52.252128 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:36:55.126836 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:36:55.275055 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_linear.rds
2025-12-16 20:36:55.311891 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_linear.rds
2025-12-16 20:36:55.337611 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_logistic.rds
2025-12-16 20:36:55.384615 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_logistic.rds
2025-12-16 20:37:04.068935 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:37:06.855477 WARNING::Fitting problem for feature 124 returning NA
2025-12-16 20:37:06.9943 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_linear.rds
2025-12-16 20:37:07.055483 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_linear.rds
2025-12-16 20:37:07.077748 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_logistic.rds
2025-12-16 20:37:07.125328 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_logistic.rds
2025-12-16 20:37:15.019529 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:37:15.048383 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:37:15.075254 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:37:15.085434 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:37:15.09931 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:37:15.129792 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:37:15.131843 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:37:15.136092 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:37:15.186413 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:37:15.188656 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:37:15.208339 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:37:15.22189 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:37:15.226176 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:37:15.241702 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:37:15.26696 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:37:20.428618 WARNING::Fitting problem for feature 50 returning NA
2025-12-16 20:37:20.457395 WARNING::Fitting problem for feature 62 returning NA
2025-12-16 20:37:20.488066 WARNING::Fitting problem for feature 74 returning NA
2025-12-16 20:37:20.49641 WARNING::Fitting problem for feature 78 returning NA
2025-12-16 20:37:20.510123 WARNING::Fitting problem for feature 84 returning NA
2025-12-16 20:37:20.54045 WARNING::Fitting problem for feature 96 returning NA
2025-12-16 20:37:20.543022 WARNING::Fitting problem for feature 97 returning NA
2025-12-16 20:37:20.547258 WARNING::Fitting problem for feature 99 returning NA
2025-12-16 20:37:20.588645 WARNING::Fitting problem for feature 114 returning NA
2025-12-16 20:37:20.591391 WARNING::Fitting problem for feature 115 returning NA
2025-12-16 20:37:20.611881 WARNING::Fitting problem for feature 123 returning NA
2025-12-16 20:37:20.628143 WARNING::Fitting problem for feature 130 returning NA
2025-12-16 20:37:20.632819 WARNING::Fitting problem for feature 132 returning NA
2025-12-16 20:37:20.647945 WARNING::Fitting problem for feature 139 returning NA
2025-12-16 20:37:20.674807 WARNING::Fitting problem for feature 150 returning NA
2025-12-16 20:37:20.79436 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_linear.rds
2025-12-16 20:37:20.831394 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_linear.rds
2025-12-16 20:37:20.865981 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/residuals_logistic.rds
2025-12-16 20:37:21.059664 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a2e902010/fits/fitted_logistic.rds
2025-12-16 20:37:29.778939 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-16 20:37:29.784575 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-16 20:37:29.788989 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-16 20:37:29.807622 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-16 20:37:29.813266 ERROR::Effect name not found in metadata: d
2025-12-16 20:37:29.817028 ERROR::No user formula provided
2025-12-16 20:37:29.827671 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-16 20:37:29.832172 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-16 20:37:31.076802 INFO::Writing function arguments to log file
2025-12-16 20:37:31.082331 INFO::Verifying options selected are valid
2025-12-16 20:37:32.024883 INFO::Writing function arguments to log file
2025-12-16 20:37:32.030529 INFO::Verifying options selected are valid
2025-12-16 20:37:32.030994 INFO::Determining format of input files
2025-12-16 20:37:32.031337 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 20:37:32.032236 INFO::Running selected normalization method: TSS
2025-12-16 20:37:32.032826 INFO::Creating output feature tables folder
2025-12-16 20:37:32.033266 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/features/data_norm.tsv
2025-12-16 20:37:32.033939 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-16 20:37:32.034257 INFO::Total samples in data: 16
2025-12-16 20:37:32.034548 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-16 20:37:32.034831 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-16 20:37:32.035531 INFO::Total filtered features: 0
2025-12-16 20:37:32.035884 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-16 20:37:32.036284 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-16 20:37:32.036607 INFO::Filtered feature names from variance filtering:
2025-12-16 20:37:32.03691 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/features/filtered_data.tsv
2025-12-16 20:37:32.037505 INFO::Running selected transform method: LOG
2025-12-16 20:37:32.037921 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/features/data_transformed.tsv
2025-12-16 20:37:32.038562 INFO::Applying z-score to standardize continuous metadata
2025-12-16 20:37:32.040838 INFO::Running the linear model component
2025-12-16 20:37:32.046481 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:32.048225 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:32.049632 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:32.052215 INFO::Counting total values for each feature
2025-12-16 20:37:32.05293 INFO::Running the logistic model component
2025-12-16 20:37:32.059069 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:32.061634 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:32.064014 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:32.067515 INFO::Counting total values for each feature
2025-12-16 20:37:32.068456 INFO::Re-running abundances for warn_prevalence
2025-12-16 20:37:32.068895 INFO::Running selected normalization method: TSS
2025-12-16 20:37:32.069457 INFO::Running selected transform method: LOG
2025-12-16 20:37:32.075172 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:32.076854 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:32.078333 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:32.12034 INFO::Creating fits folder
2025-12-16 20:37:32.121118 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/fits/residuals_linear.rds
2025-12-16 20:37:32.12176 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/fits/fitted_linear.rds
2025-12-16 20:37:32.122308 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/fits/residuals_logistic.rds
2025-12-16 20:37:32.122829 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/fits/fitted_logistic.rds
2025-12-16 20:37:32.123987 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/all_results.tsv
2025-12-16 20:37:32.124777 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//RtmppgdEqd/file1035a146ca089/significant_results.tsv
2025-12-16 20:37:32.125384 INFO::Creating output figures folder
2025-12-16 20:37:32.125967 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/figures/summary_plot.pdf
2025-12-16 20:37:32.803723 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/figures
2025-12-16 20:37:32.804719 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 20:37:32.807041 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 20:37:33.025766 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/figures/summary_plot.pdf
2025-12-16 20:37:33.709693 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a146ca089/figures
2025-12-16 20:37:33.71031 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 20:37:33.712175 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 20:37:33.937664 INFO::Running the linear model component
2025-12-16 20:37:33.940597 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:33.942353 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:33.943908 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:33.946781 INFO::Counting total values for each feature
2025-12-16 20:37:33.947486 INFO::Running the logistic model component
2025-12-16 20:37:33.950771 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:33.95313 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:33.955118 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:33.958136 INFO::Counting total values for each feature
2025-12-16 20:37:33.958891 INFO::Re-running abundances for warn_prevalence
2025-12-16 20:37:33.959168 INFO::Running selected normalization method: TSS
2025-12-16 20:37:33.959646 INFO::Running selected transform method: LOG
2025-12-16 20:37:33.962666 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:33.964114 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:33.965418 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:33.995177 INFO::Creating output folder
2025-12-16 20:37:33.995648 INFO::Creating output figures folder
2025-12-16 20:37:33.996109 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a7d4de769/figures/summary_plot.pdf
2025-12-16 20:37:34.652844 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a7d4de769/figures
2025-12-16 20:37:34.653503 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-16 20:37:34.655286 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-16 20:37:35.084378 INFO::Applying z-score to standardize continuous metadata
2025-12-16 20:37:35.087275 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-16 20:37:35.087572 INFO::Bypass z-score application to metadata
2025-12-16 20:37:35.08839 INFO::Bypass z-score application to metadata
2025-12-16 20:37:35.09565 INFO::Determining format of input files
2025-12-16 20:37:35.095961 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 20:37:35.096212 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-16 20:37:35.09849 INFO::Determining format of input files
2025-12-16 20:37:35.098805 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-16 20:37:35.099204 INFO::Input format is feature_specific_covariate samples as columns
2025-12-16 20:37:35.101767 INFO::Determining format of input files
2025-12-16 20:37:35.102048 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-16 20:37:35.102352 INFO::Input format is feature_specific_covariate samples as columns
2025-12-16 20:37:35.102812 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-16 20:37:35.10303 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-16 20:37:35.106927 INFO::Running selected transform method: LOG
2025-12-16 20:37:35.107296 INFO::Creating output feature tables folder
2025-12-16 20:37:35.107708 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a3940f026/features/data_transformed.tsv
2025-12-16 20:37:35.112048 INFO::Running selected transform method: LOG
2025-12-16 20:37:35.112533 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a3940f026/features/data_transformed.tsv
2025-12-16 20:37:35.114316 INFO::Running selected transform method: PLOG
2025-12-16 20:37:35.114954 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a3940f026/features/data_transformed.tsv
2025-12-16 20:37:35.116157 INFO::Running selected transform method: NONE
2025-12-16 20:37:35.116445 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a3940f026/features/data_transformed.tsv
2025-12-16 20:37:35.119594 INFO::Running the linear model component
2025-12-16 20:37:35.122718 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:35.124326 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:35.125741 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:35.128251 INFO::Counting total values for each feature
2025-12-16 20:37:35.128848 INFO::Running the logistic model component
2025-12-16 20:37:35.131545 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:35.133581 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:35.135357 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:35.138113 INFO::Counting total values for each feature
2025-12-16 20:37:35.138825 INFO::Re-running abundances for warn_prevalence
2025-12-16 20:37:35.139092 INFO::Running selected normalization method: TSS
2025-12-16 20:37:35.13955 INFO::Running selected transform method: LOG
2025-12-16 20:37:35.143007 INFO::Fitting model to feature number 1, a
2025-12-16 20:37:35.144531 INFO::Fitting model to feature number 2, b
2025-12-16 20:37:35.145829 INFO::Fitting model to feature number 3, c
2025-12-16 20:37:35.176332 INFO::Creating output folder
2025-12-16 20:37:35.176802 INFO::Creating fits folder
2025-12-16 20:37:35.17712 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a56566c27/fits/residuals_linear.rds
2025-12-16 20:37:35.177604 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a56566c27/fits/fitted_linear.rds
2025-12-16 20:37:35.178004 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a56566c27/fits/residuals_logistic.rds
2025-12-16 20:37:35.178484 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a56566c27/fits/fitted_logistic.rds
2025-12-16 20:37:35.179574 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmppgdEqd/file1035a56566c27/all_results.tsv
2025-12-16 20:37:35.180331 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//RtmppgdEqd/file1035a56566c27/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.253 4.250 156.501
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.349 | 0.549 | 9.126 | |
| maaslin_check_arguments | 0.063 | 0.002 | 0.065 | |
| maaslin_check_formula | 0.063 | 0.004 | 0.068 | |
| maaslin_compute_formula | 0.074 | 0.004 | 0.080 | |
| maaslin_contrast_test | 7.445 | 0.684 | 8.562 | |
| maaslin_filter | 0.244 | 0.024 | 0.277 | |
| maaslin_fit | 5.152 | 0.549 | 5.962 | |
| maaslin_log_arguments | 0.057 | 0.003 | 0.061 | |
| maaslin_normalize | 0.139 | 0.021 | 0.173 | |
| maaslin_plot_results | 16.962 | 0.675 | 18.441 | |
| maaslin_plot_results_from_output | 17.056 | 0.792 | 18.526 | |
| maaslin_process_metadata | 0.239 | 0.017 | 0.272 | |
| maaslin_read_data | 0.055 | 0.004 | 0.059 | |
| maaslin_reorder_data | 0.055 | 0.003 | 0.059 | |
| maaslin_transform | 0.287 | 0.029 | 0.332 | |
| maaslin_write_results | 5.710 | 0.591 | 6.687 | |
| maaslin_write_results_lefse_format | 5.508 | 0.400 | 6.189 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.001 | 0.001 | |