William Nickols
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 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 2025-11-11 12:03 -0500 (Tue, 11 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: 2025-11-10 20:47:10 -0500 (Mon, 10 Nov 2025) |
| EndedAt: 2025-11-10 20:52:00 -0500 (Mon, 10 Nov 2025) |
| EllapsedTime: 290.8 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_1.2.0.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 16.711 0.666 17.608
maaslin_plot_results 16.014 0.706 16.764
maaslin3 8.354 0.531 8.971
maaslin_contrast_test 7.184 0.675 7.946
maaslin_write_results_lefse_format 5.493 0.477 6.009
maaslin_write_results 5.121 0.611 5.767
maaslin_fit 4.995 0.549 5.572
* 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")
2025-11-10 20:49:36.965657 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:49:37.306167 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:49:37.336293 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:49:37.344254 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:49:37.356504 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:49:37.388436 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:49:37.390397 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:49:37.394307 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:49:37.426298 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:49:37.428319 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:49:37.445592 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:49:37.459972 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:49:37.469543 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:49:37.48334 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:49:37.506367 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:49:43.9877 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:49:44.016215 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:49:44.043977 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:49:44.052076 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:49:44.064177 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:49:44.091426 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:49:44.093543 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:49:44.097939 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:49:44.144471 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:49:44.146454 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:49:44.163118 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:49:44.176538 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:49:44.180735 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:49:44.194259 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:49:44.217211 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:49:45.663 R[7846:680954936] XType: Using static font registry.
2025-11-10 20:49:53.276602 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:49:53.306791 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:49:53.334537 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:49:53.342721 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:49:53.355393 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:49:53.382242 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:49:53.384283 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:49:53.388483 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:49:53.839859 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:49:53.842157 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:49:53.860682 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:49:53.875905 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:49:53.880688 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:49:53.896065 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:49:53.922332 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:49:59.235689 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:49:59.262742 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:49:59.288758 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:49:59.296439 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:49:59.30864 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:49:59.33621 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:49:59.338309 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:49:59.342527 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:49:59.3746 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:49:59.376646 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:49:59.393937 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:49:59.407503 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:49:59.411951 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:49:59.42561 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:49:59.448612 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:49:59.526384 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/residuals_linear.rds
2025-11-10 20:49:59.559268 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/fitted_linear.rds
2025-11-10 20:49:59.59362 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/residuals_logistic.rds
2025-11-10 20:49:59.762878 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/fitted_logistic.rds
2025-11-10 20:50:08.002649 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:50:08.02983 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:50:08.056111 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:50:08.063927 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:50:08.075945 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:50:08.102558 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:50:08.104554 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:50:08.108704 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:50:08.142256 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:50:08.144301 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:50:08.161252 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:50:08.175696 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:50:08.179986 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:50:08.193964 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:50:08.218432 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:50:13.706219 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:50:13.733569 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:50:13.759746 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:50:13.767917 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:50:13.78063 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:50:13.806437 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:50:13.808305 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:50:13.812222 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:50:13.843634 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:50:13.845747 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:50:13.86301 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:50:13.876854 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:50:13.881048 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:50:13.894762 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:50:13.918554 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:50:13.994081 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/residuals_linear.rds
2025-11-10 20:50:14.024785 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/fitted_linear.rds
2025-11-10 20:50:14.05835 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/residuals_logistic.rds
2025-11-10 20:50:14.224573 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/fitted_logistic.rds
2025-11-10 20:50:22.353091 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:50:22.379323 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:50:22.405069 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:50:22.412685 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:50:22.424633 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:50:22.45152 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:50:22.453618 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:50:22.457832 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:50:22.49213 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:50:22.494269 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:50:22.512773 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:50:22.527426 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:50:22.531879 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:50:22.546708 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:50:22.572562 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:50:27.834447 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:50:27.861346 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:50:27.888526 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:50:27.8969 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:50:27.909339 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:50:27.936837 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:50:27.93897 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:50:27.943338 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:50:27.978631 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:50:27.981163 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:50:28.000821 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:50:28.015772 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:50:28.020561 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:50:28.035875 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:50:28.066192 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:50:28.173596 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/residuals_linear.rds
2025-11-10 20:50:28.206891 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/fitted_linear.rds
2025-11-10 20:50:28.241129 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/residuals_logistic.rds
2025-11-10 20:50:28.409715 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6f2d77a4/fits/fitted_logistic.rds
2025-11-10 20:50:36.5754 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:50:36.60294 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:50:36.62956 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:50:36.637746 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:50:36.650518 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:50:36.678442 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:50:36.680614 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:50:36.685039 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:50:36.720561 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:50:36.722735 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:50:36.740353 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:50:36.754788 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:50:36.759325 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:50:36.774737 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:50:36.800981 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:50:41.962353 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:50:41.988378 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:50:42.01367 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:50:42.021848 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:50:42.033998 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:50:42.087093 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:50:42.089146 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:50:42.093251 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:50:42.125871 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:50:42.127878 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:50:42.144546 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:50:42.157797 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:50:42.161897 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:50:42.175133 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:50:42.198153 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:50:51.215539 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:50:55.235676 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:04.479731 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:08.265052 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:08.448592 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_linear.rds
2025-11-10 20:51:08.480996 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_linear.rds
2025-11-10 20:51:08.503292 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_logistic.rds
2025-11-10 20:51:08.543654 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_logistic.rds
2025-11-10 20:51:17.237769 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:19.97095 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:20.083464 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_linear.rds
2025-11-10 20:51:20.116572 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_linear.rds
2025-11-10 20:51:20.138983 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_logistic.rds
2025-11-10 20:51:20.179424 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_logistic.rds
2025-11-10 20:51:27.940396 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:30.042573 WARNING::Fitting problem for feature 124 returning NA
2025-11-10 20:51:30.142756 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_linear.rds
2025-11-10 20:51:30.17558 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_linear.rds
2025-11-10 20:51:30.198334 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_logistic.rds
2025-11-10 20:51:30.238999 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_logistic.rds
2025-11-10 20:51:38.14238 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:51:38.170474 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:51:38.197366 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:51:38.205679 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:51:38.218647 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:51:38.24689 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:51:38.24922 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:51:38.253521 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:51:38.289888 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:51:38.292259 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:51:38.309969 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:51:38.324159 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:51:38.32855 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:51:38.343087 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:51:38.36741 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:51:43.625962 WARNING::Fitting problem for feature 50 returning NA
2025-11-10 20:51:43.652361 WARNING::Fitting problem for feature 62 returning NA
2025-11-10 20:51:43.678404 WARNING::Fitting problem for feature 74 returning NA
2025-11-10 20:51:43.686389 WARNING::Fitting problem for feature 78 returning NA
2025-11-10 20:51:43.698614 WARNING::Fitting problem for feature 84 returning NA
2025-11-10 20:51:43.726157 WARNING::Fitting problem for feature 96 returning NA
2025-11-10 20:51:43.728261 WARNING::Fitting problem for feature 97 returning NA
2025-11-10 20:51:43.732456 WARNING::Fitting problem for feature 99 returning NA
2025-11-10 20:51:43.766565 WARNING::Fitting problem for feature 114 returning NA
2025-11-10 20:51:43.768672 WARNING::Fitting problem for feature 115 returning NA
2025-11-10 20:51:43.785852 WARNING::Fitting problem for feature 123 returning NA
2025-11-10 20:51:43.800106 WARNING::Fitting problem for feature 130 returning NA
2025-11-10 20:51:43.804578 WARNING::Fitting problem for feature 132 returning NA
2025-11-10 20:51:43.818891 WARNING::Fitting problem for feature 139 returning NA
2025-11-10 20:51:43.844224 WARNING::Fitting problem for feature 150 returning NA
2025-11-10 20:51:43.940411 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_linear.rds
2025-11-10 20:51:43.973346 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_linear.rds
2025-11-10 20:51:44.007244 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/residuals_logistic.rds
2025-11-10 20:51:44.175512 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea635a4b4b2/fits/fitted_logistic.rds
2025-11-10 20:51:51.944243 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-10 20:51:51.949825 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-10 20:51:51.953607 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-10 20:51:51.9716 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-10 20:51:51.977693 ERROR::Effect name not found in metadata: d
2025-11-10 20:51:51.982493 ERROR::No user formula provided
2025-11-10 20:51:51.992699 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-10 20:51:51.996705 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-10 20:51:53.126324 INFO::Writing function arguments to log file
2025-11-10 20:51:53.132377 INFO::Verifying options selected are valid
2025-11-10 20:51:54.008632 INFO::Writing function arguments to log file
2025-11-10 20:51:54.013009 INFO::Verifying options selected are valid
2025-11-10 20:51:54.013377 INFO::Determining format of input files
2025-11-10 20:51:54.013684 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-10 20:51:54.014444 INFO::Running selected normalization method: TSS
2025-11-10 20:51:54.014961 INFO::Creating output feature tables folder
2025-11-10 20:51:54.015337 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/features/data_norm.tsv
2025-11-10 20:51:54.015928 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-10 20:51:54.016222 INFO::Total samples in data: 16
2025-11-10 20:51:54.016506 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-10 20:51:54.016782 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-10 20:51:54.017414 INFO::Total filtered features: 0
2025-11-10 20:51:54.017736 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-10 20:51:54.018114 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-10 20:51:54.01842 INFO::Filtered feature names from variance filtering:
2025-11-10 20:51:54.018704 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/features/filtered_data.tsv
2025-11-10 20:51:54.019242 INFO::Running selected transform method: LOG
2025-11-10 20:51:54.019628 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/features/data_transformed.tsv
2025-11-10 20:51:54.020217 INFO::Applying z-score to standardize continuous metadata
2025-11-10 20:51:54.023722 INFO::Running the linear model component
2025-11-10 20:51:54.028835 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:54.03038 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:54.031714 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:54.034132 INFO::Counting total values for each feature
2025-11-10 20:51:54.034787 INFO::Running the logistic model component
2025-11-10 20:51:54.039483 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:54.041556 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:54.043446 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:54.046326 INFO::Counting total values for each feature
2025-11-10 20:51:54.047095 INFO::Re-running abundances for warn_prevalence
2025-11-10 20:51:54.047461 INFO::Running selected normalization method: TSS
2025-11-10 20:51:54.047952 INFO::Running selected transform method: LOG
2025-11-10 20:51:54.052727 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:54.054141 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:54.055442 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:54.095649 INFO::Creating fits folder
2025-11-10 20:51:54.096299 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/fits/residuals_linear.rds
2025-11-10 20:51:54.096856 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/fits/fitted_linear.rds
2025-11-10 20:51:54.097331 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/fits/residuals_logistic.rds
2025-11-10 20:51:54.097803 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/fits/fitted_logistic.rds
2025-11-10 20:51:54.098798 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/all_results.tsv
2025-11-10 20:51:54.099489 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//RtmpyrafIM/file1ea63cae8c7b/significant_results.tsv
2025-11-10 20:51:54.100001 INFO::Creating output figures folder
2025-11-10 20:51:54.100482 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/figures/summary_plot.pdf
2025-11-10 20:51:54.721772 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/figures
2025-11-10 20:51:54.722717 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-10 20:51:54.725185 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-10 20:51:54.930382 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/figures/summary_plot.pdf
2025-11-10 20:51:55.52044 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea63cae8c7b/figures
2025-11-10 20:51:55.521003 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-10 20:51:55.522786 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-10 20:51:55.7163 INFO::Running the linear model component
2025-11-10 20:51:55.719101 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:55.720546 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:55.721758 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:55.72405 INFO::Counting total values for each feature
2025-11-10 20:51:55.724602 INFO::Running the logistic model component
2025-11-10 20:51:55.727187 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:55.729118 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:55.730843 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:55.733458 INFO::Counting total values for each feature
2025-11-10 20:51:55.7341 INFO::Re-running abundances for warn_prevalence
2025-11-10 20:51:55.734334 INFO::Running selected normalization method: TSS
2025-11-10 20:51:55.734744 INFO::Running selected transform method: LOG
2025-11-10 20:51:55.737316 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:55.738612 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:55.739793 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:55.766061 INFO::Creating output folder
2025-11-10 20:51:55.766494 INFO::Creating output figures folder
2025-11-10 20:51:55.766924 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6701eb51d/figures/summary_plot.pdf
2025-11-10 20:51:56.355146 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6701eb51d/figures
2025-11-10 20:51:56.355777 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-10 20:51:56.357931 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-10 20:51:56.753367 INFO::Applying z-score to standardize continuous metadata
2025-11-10 20:51:56.756337 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-10 20:51:56.756682 INFO::Bypass z-score application to metadata
2025-11-10 20:51:56.757622 INFO::Bypass z-score application to metadata
2025-11-10 20:51:56.765775 INFO::Determining format of input files
2025-11-10 20:51:56.766156 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-10 20:51:56.766439 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-10 20:51:56.768724 INFO::Determining format of input files
2025-11-10 20:51:56.76909 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-10 20:51:56.769491 INFO::Input format is feature_specific_covariate samples as columns
2025-11-10 20:51:56.771882 INFO::Determining format of input files
2025-11-10 20:51:56.772167 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-10 20:51:56.772462 INFO::Input format is feature_specific_covariate samples as columns
2025-11-10 20:51:56.772916 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-10 20:51:56.773141 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-10 20:51:56.776728 INFO::Running selected transform method: LOG
2025-11-10 20:51:56.777071 INFO::Creating output feature tables folder
2025-11-10 20:51:56.777442 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea65829ecb9/features/data_transformed.tsv
2025-11-10 20:51:56.778752 INFO::Running selected transform method: LOG
2025-11-10 20:51:56.779084 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea65829ecb9/features/data_transformed.tsv
2025-11-10 20:51:56.780239 INFO::Running selected transform method: PLOG
2025-11-10 20:51:56.78072 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea65829ecb9/features/data_transformed.tsv
2025-11-10 20:51:56.781784 INFO::Running selected transform method: NONE
2025-11-10 20:51:56.782054 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea65829ecb9/features/data_transformed.tsv
2025-11-10 20:51:56.785027 INFO::Running the linear model component
2025-11-10 20:51:56.787766 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:56.789203 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:56.790413 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:56.792689 INFO::Counting total values for each feature
2025-11-10 20:51:56.79322 INFO::Running the logistic model component
2025-11-10 20:51:56.795713 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:56.797568 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:56.799316 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:56.801996 INFO::Counting total values for each feature
2025-11-10 20:51:56.802656 INFO::Re-running abundances for warn_prevalence
2025-11-10 20:51:56.802889 INFO::Running selected normalization method: TSS
2025-11-10 20:51:56.803319 INFO::Running selected transform method: LOG
2025-11-10 20:51:56.805954 INFO::Fitting model to feature number 1, a
2025-11-10 20:51:56.807308 INFO::Fitting model to feature number 2, b
2025-11-10 20:51:56.808508 INFO::Fitting model to feature number 3, c
2025-11-10 20:51:56.835545 INFO::Creating output folder
2025-11-10 20:51:56.835946 INFO::Creating fits folder
2025-11-10 20:51:56.83624 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6287492e7/fits/residuals_linear.rds
2025-11-10 20:51:56.836679 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6287492e7/fits/fitted_linear.rds
2025-11-10 20:51:56.837071 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6287492e7/fits/residuals_logistic.rds
2025-11-10 20:51:56.837464 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6287492e7/fits/fitted_logistic.rds
2025-11-10 20:51:56.838341 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpyrafIM/file1ea6287492e7/all_results.tsv
2025-11-10 20:51:56.838905 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//RtmpyrafIM/file1ea6287492e7/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
137.462 5.570 144.085
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.354 | 0.531 | 8.971 | |
| maaslin_check_arguments | 0.064 | 0.002 | 0.065 | |
| maaslin_check_formula | 0.059 | 0.004 | 0.062 | |
| maaslin_compute_formula | 0.056 | 0.003 | 0.059 | |
| maaslin_contrast_test | 7.184 | 0.675 | 7.946 | |
| maaslin_filter | 0.223 | 0.031 | 0.258 | |
| maaslin_fit | 4.995 | 0.549 | 5.572 | |
| maaslin_log_arguments | 0.057 | 0.004 | 0.060 | |
| maaslin_normalize | 0.127 | 0.009 | 0.137 | |
| maaslin_plot_results | 16.014 | 0.706 | 16.764 | |
| maaslin_plot_results_from_output | 16.711 | 0.666 | 17.608 | |
| maaslin_process_metadata | 0.218 | 0.020 | 0.239 | |
| maaslin_read_data | 0.050 | 0.002 | 0.053 | |
| maaslin_reorder_data | 0.052 | 0.003 | 0.055 | |
| maaslin_transform | 0.270 | 0.027 | 0.310 | |
| maaslin_write_results | 5.121 | 0.611 | 5.767 | |
| maaslin_write_results_lefse_format | 5.493 | 0.477 | 6.009 | |
| preprocess_dna_mtx | 0.001 | 0.001 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.002 | |