William Nickols
| Snapshot Date: 2025-09-10 13:45 -0400 (Wed, 10 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-11 12:06 -0400 (Thu, 11 Sep 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" | 4539 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4474 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
| 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 1150/2322 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2025-09-10 21:05:38 -0400 (Wed, 10 Sep 2025) |
| EndedAt: 2025-09-10 21:10:05 -0400 (Wed, 10 Sep 2025) |
| EllapsedTime: 267.3 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_1.1.0.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 ‘1.1.0’
* 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 13.797 0.615 14.803
maaslin_plot_results 13.550 0.675 14.254
maaslin3 8.223 0.424 8.665
maaslin_contrast_test 7.094 0.640 7.776
maaslin_write_results 5.836 0.606 6.882
maaslin_write_results_lefse_format 5.343 0.509 5.900
maaslin_fit 5.233 0.564 5.877
* 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 ‘1.1.0’ ** 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")
2025-09-10 21:08:00.938555 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:00.965267 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:00.993638 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:01.001057 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:01.017464 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:01.043259 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:01.04517 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:01.049105 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:01.086519 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:01.088394 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:01.104847 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:01.118282 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:01.122446 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:01.135889 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:01.163404 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:07.373955 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:07.400918 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:07.42653 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:07.434135 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:07.445985 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:07.473311 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:07.47556 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:07.479934 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:07.515069 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:07.517222 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:07.546031 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:07.559618 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:07.563896 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:07.577871 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:07.60175 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:08.777 R[32227:212712605] XType: Using static font registry.
2025-09-10 21:08:15.268909 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:15.296418 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:15.32268 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:15.330832 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:15.34307 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:15.369989 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:15.372042 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:15.376324 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:15.424673 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:15.426663 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:15.443534 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:15.457647 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:15.46202 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:15.475956 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:15.500405 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:20.939387 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:20.965799 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:20.991548 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:20.99916 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:21.011097 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:21.03737 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:21.039359 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:21.043645 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:21.079345 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:21.081553 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:21.100136 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:21.11512 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:21.119799 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:21.134949 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:21.160863 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:21.240113 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/residuals_linear.rds
2025-09-10 21:08:21.272519 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/fitted_linear.rds
2025-09-10 21:08:21.306721 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/residuals_logistic.rds
2025-09-10 21:08:21.493739 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/fitted_logistic.rds
2025-09-10 21:08:27.792205 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:27.830432 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:27.856185 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:27.863941 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:27.876142 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:27.902696 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:27.904761 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:27.908996 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:27.941618 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:27.943726 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:27.960733 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:27.974356 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:27.978546 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:27.99228 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:28.016362 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:33.148374 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:33.175014 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:33.200951 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:33.20868 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:33.22068 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:33.247222 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:33.249216 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:33.253382 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:33.287041 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:33.289273 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:33.307879 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:33.322517 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:33.327037 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:33.342265 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:33.368152 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:33.460673 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/residuals_linear.rds
2025-09-10 21:08:33.490865 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/fitted_linear.rds
2025-09-10 21:08:33.522086 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/residuals_logistic.rds
2025-09-10 21:08:33.68666 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/fitted_logistic.rds
2025-09-10 21:08:40.0697 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:40.094023 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:40.117823 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:40.12493 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:40.136149 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:40.160296 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:40.162104 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:40.165826 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:40.195928 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:40.197798 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:40.213375 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:40.237561 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:40.241293 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:40.253245 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:40.273486 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:45.112356 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:45.138085 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:45.163396 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:45.171089 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:45.182835 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:45.208745 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:45.210724 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:45.2148 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:45.246854 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:45.248847 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:45.265426 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:45.278988 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:45.283387 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:45.297107 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:45.320508 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:45.395932 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/residuals_linear.rds
2025-09-10 21:08:45.428404 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/fitted_linear.rds
2025-09-10 21:08:45.462258 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/residuals_logistic.rds
2025-09-10 21:08:45.630288 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de322355834/fits/fitted_logistic.rds
2025-09-10 21:08:52.090411 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:52.116034 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:52.141706 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:52.149358 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:52.161367 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:52.187232 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:52.18922 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:52.193327 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:52.226263 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:52.228296 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:52.245112 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:52.258792 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:52.262976 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:52.276761 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:52.300301 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:08:57.273116 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:08:57.299708 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:08:57.326091 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:08:57.333872 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:08:57.346782 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:08:57.374324 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:08:57.376374 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:08:57.380481 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:08:57.414494 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:08:57.416542 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:08:57.433829 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:08:57.448254 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:08:57.452963 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:08:57.468882 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:08:57.495585 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:09:04.787126 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:08.55338 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:16.224382 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:19.981953 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:20.165705 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_linear.rds
2025-09-10 21:09:20.198273 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_linear.rds
2025-09-10 21:09:20.220082 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_logistic.rds
2025-09-10 21:09:20.259253 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_logistic.rds
2025-09-10 21:09:27.382377 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:29.991625 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:30.090466 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_linear.rds
2025-09-10 21:09:30.123267 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_linear.rds
2025-09-10 21:09:30.145581 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_logistic.rds
2025-09-10 21:09:30.185681 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_logistic.rds
2025-09-10 21:09:36.193256 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:38.843074 WARNING::Fitting problem for feature 124 returning NA
2025-09-10 21:09:38.940741 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_linear.rds
2025-09-10 21:09:38.973906 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_linear.rds
2025-09-10 21:09:38.995837 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_logistic.rds
2025-09-10 21:09:39.035615 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_logistic.rds
2025-09-10 21:09:44.856372 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:09:44.893241 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:09:44.920339 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:09:44.928335 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:09:44.940516 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:09:44.968092 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:09:44.970627 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:09:44.975093 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:09:45.009102 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:09:45.011251 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:09:45.028402 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:09:45.043015 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:09:45.047416 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:09:45.061982 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:09:45.085605 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:09:50.161446 WARNING::Fitting problem for feature 50 returning NA
2025-09-10 21:09:50.187761 WARNING::Fitting problem for feature 62 returning NA
2025-09-10 21:09:50.213761 WARNING::Fitting problem for feature 74 returning NA
2025-09-10 21:09:50.221672 WARNING::Fitting problem for feature 78 returning NA
2025-09-10 21:09:50.233622 WARNING::Fitting problem for feature 84 returning NA
2025-09-10 21:09:50.263381 WARNING::Fitting problem for feature 96 returning NA
2025-09-10 21:09:50.265667 WARNING::Fitting problem for feature 97 returning NA
2025-09-10 21:09:50.270382 WARNING::Fitting problem for feature 99 returning NA
2025-09-10 21:09:50.30367 WARNING::Fitting problem for feature 114 returning NA
2025-09-10 21:09:50.305721 WARNING::Fitting problem for feature 115 returning NA
2025-09-10 21:09:50.322664 WARNING::Fitting problem for feature 123 returning NA
2025-09-10 21:09:50.336933 WARNING::Fitting problem for feature 130 returning NA
2025-09-10 21:09:50.341271 WARNING::Fitting problem for feature 132 returning NA
2025-09-10 21:09:50.356271 WARNING::Fitting problem for feature 139 returning NA
2025-09-10 21:09:50.383327 WARNING::Fitting problem for feature 150 returning NA
2025-09-10 21:09:50.499071 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_linear.rds
2025-09-10 21:09:50.531267 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_linear.rds
2025-09-10 21:09:50.564793 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/residuals_logistic.rds
2025-09-10 21:09:50.737193 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3668f4044/fits/fitted_logistic.rds
2025-09-10 21:09:57.096738 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-10 21:09:57.102377 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-10 21:09:57.106178 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-10 21:09:57.123657 ERROR::No fixed, group, or
ordered effects included in formula.
2025-09-10 21:09:57.129363 ERROR::Effect name not found in metadata: d
2025-09-10 21:09:57.135461 ERROR::No user formula provided
2025-09-10 21:09:57.145119 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-10 21:09:57.14888 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-09-10 21:09:58.150458 INFO::Writing function arguments to log file
2025-09-10 21:09:58.155629 INFO::Verifying options selected are valid
2025-09-10 21:09:58.834951 INFO::Writing function arguments to log file
2025-09-10 21:09:58.839198 INFO::Verifying options selected are valid
2025-09-10 21:09:58.839567 INFO::Determining format of input files
2025-09-10 21:09:58.839863 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 21:09:58.840663 INFO::Running selected normalization method: TSS
2025-09-10 21:09:58.841172 INFO::Creating output feature tables folder
2025-09-10 21:09:58.841553 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/features/data_norm.tsv
2025-09-10 21:09:58.842127 INFO::Filter data based on min abundance and min prevalence
2025-09-10 21:09:58.842436 INFO::Total samples in data: 16
2025-09-10 21:09:58.842711 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-10 21:09:58.843295 INFO::Total filtered features: 0
2025-09-10 21:09:58.843632 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-10 21:09:58.843999 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-10 21:09:58.844293 INFO::Filtered feature names from variance filtering:
2025-09-10 21:09:58.84457 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/features/filtered_data.tsv
2025-09-10 21:09:58.84508 INFO::Running selected transform method: LOG
2025-09-10 21:09:58.84545 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/features/data_transformed.tsv
2025-09-10 21:09:58.846006 INFO::Applying z-score to standardize continuous metadata
2025-09-10 21:09:58.847875 INFO::Running the linear model component
2025-09-10 21:09:58.852776 INFO::Fitting model to feature number 1, a
2025-09-10 21:09:58.854203 INFO::Fitting model to feature number 2, b
2025-09-10 21:09:58.855483 INFO::Fitting model to feature number 3, c
2025-09-10 21:09:58.857749 INFO::Counting total values for each feature
2025-09-10 21:09:58.858384 INFO::Running the logistic model component
2025-09-10 21:09:58.863181 INFO::Fitting model to feature number 1, a
2025-09-10 21:09:58.865251 INFO::Fitting model to feature number 2, b
2025-09-10 21:09:58.867134 INFO::Fitting model to feature number 3, c
2025-09-10 21:09:58.869997 INFO::Counting total values for each feature
2025-09-10 21:09:58.870759 INFO::Re-running abundances for warn_prevalence
2025-09-10 21:09:58.871072 INFO::Running selected normalization method: TSS
2025-09-10 21:09:58.871556 INFO::Running selected transform method: LOG
2025-09-10 21:09:58.876491 INFO::Fitting model to feature number 1, a
2025-09-10 21:09:58.877875 INFO::Fitting model to feature number 2, b
2025-09-10 21:09:58.879202 INFO::Fitting model to feature number 3, c
2025-09-10 21:09:58.90508 INFO::Creating fits folder
2025-09-10 21:09:58.905619 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/fits/residuals_linear.rds
2025-09-10 21:09:58.906134 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/fits/fitted_linear.rds
2025-09-10 21:09:58.906612 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/fits/residuals_logistic.rds
2025-09-10 21:09:58.907064 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/fits/fitted_logistic.rds
2025-09-10 21:09:58.907985 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/all_results.tsv
2025-09-10 21:09:58.908637 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//RtmpfGHQCw/file7de3428166cc/significant_results.tsv
2025-09-10 21:09:58.909144 INFO::Creating output figures folder
2025-09-10 21:09:58.909612 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/figures/summary_plot.pdf
2025-09-10 21:09:59.380352 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/figures
2025-09-10 21:09:59.381117 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 21:09:59.383035 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 21:09:59.534733 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/figures/summary_plot.pdf
2025-09-10 21:09:59.99737 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de3428166cc/figures
2025-09-10 21:09:59.997923 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 21:09:59.999657 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 21:10:00.157483 INFO::Running the linear model component
2025-09-10 21:10:00.160208 INFO::Fitting model to feature number 1, a
2025-09-10 21:10:00.161571 INFO::Fitting model to feature number 2, b
2025-09-10 21:10:00.16273 INFO::Fitting model to feature number 3, c
2025-09-10 21:10:00.16495 INFO::Counting total values for each feature
2025-09-10 21:10:00.165491 INFO::Running the logistic model component
2025-09-10 21:10:00.167963 INFO::Fitting model to feature number 1, a
2025-09-10 21:10:00.16981 INFO::Fitting model to feature number 2, b
2025-09-10 21:10:00.171473 INFO::Fitting model to feature number 3, c
2025-09-10 21:10:00.174051 INFO::Counting total values for each feature
2025-09-10 21:10:00.17468 INFO::Re-running abundances for warn_prevalence
2025-09-10 21:10:00.174908 INFO::Running selected normalization method: TSS
2025-09-10 21:10:00.175305 INFO::Running selected transform method: LOG
2025-09-10 21:10:00.177822 INFO::Fitting model to feature number 1, a
2025-09-10 21:10:00.179061 INFO::Fitting model to feature number 2, b
2025-09-10 21:10:00.180185 INFO::Fitting model to feature number 3, c
2025-09-10 21:10:00.205691 INFO::Creating output folder
2025-09-10 21:10:00.206094 INFO::Creating output figures folder
2025-09-10 21:10:00.206508 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de37ed5aed4/figures/summary_plot.pdf
2025-09-10 21:10:00.668778 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de37ed5aed4/figures
2025-09-10 21:10:00.669342 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-10 21:10:00.671062 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-10 21:10:01.007736 INFO::Applying z-score to standardize continuous metadata
2025-09-10 21:10:01.010217 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-10 21:10:01.010473 INFO::Bypass z-score application to metadata
2025-09-10 21:10:01.011176 INFO::Bypass z-score application to metadata
2025-09-10 21:10:01.017172 INFO::Determining format of input files
2025-09-10 21:10:01.017478 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 21:10:01.017712 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-10 21:10:01.019761 INFO::Determining format of input files
2025-09-10 21:10:01.020066 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-10 21:10:01.020429 INFO::Input format is feature_specific_covariate samples as columns
2025-09-10 21:10:01.022683 INFO::Determining format of input files
2025-09-10 21:10:01.022955 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-10 21:10:01.023236 INFO::Input format is feature_specific_covariate samples as columns
2025-09-10 21:10:01.023665 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-10 21:10:01.023869 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-10 21:10:01.027131 INFO::Running selected transform method: LOG
2025-09-10 21:10:01.027459 INFO::Creating output feature tables folder
2025-09-10 21:10:01.027802 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de36df9e599/features/data_transformed.tsv
2025-09-10 21:10:01.029001 INFO::Running selected transform method: LOG
2025-09-10 21:10:01.029301 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de36df9e599/features/data_transformed.tsv
2025-09-10 21:10:01.030376 INFO::Running selected transform method: PLOG
2025-09-10 21:10:01.03084 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de36df9e599/features/data_transformed.tsv
2025-09-10 21:10:01.031672 INFO::Running selected transform method: NONE
2025-09-10 21:10:01.031896 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de36df9e599/features/data_transformed.tsv
2025-09-10 21:10:01.034316 INFO::Running the linear model component
2025-09-10 21:10:01.036852 INFO::Fitting model to feature number 1, a
2025-09-10 21:10:01.038149 INFO::Fitting model to feature number 2, b
2025-09-10 21:10:01.039295 INFO::Fitting model to feature number 3, c
2025-09-10 21:10:01.04144 INFO::Counting total values for each feature
2025-09-10 21:10:01.041956 INFO::Running the logistic model component
2025-09-10 21:10:01.044394 INFO::Fitting model to feature number 1, a
2025-09-10 21:10:01.046243 INFO::Fitting model to feature number 2, b
2025-09-10 21:10:01.047967 INFO::Fitting model to feature number 3, c
2025-09-10 21:10:01.05059 INFO::Counting total values for each feature
2025-09-10 21:10:01.051249 INFO::Re-running abundances for warn_prevalence
2025-09-10 21:10:01.05149 INFO::Running selected normalization method: TSS
2025-09-10 21:10:01.051897 INFO::Running selected transform method: LOG
2025-09-10 21:10:01.054473 INFO::Fitting model to feature number 1, a
2025-09-10 21:10:01.0557 INFO::Fitting model to feature number 2, b
2025-09-10 21:10:01.056859 INFO::Fitting model to feature number 3, c
2025-09-10 21:10:01.082291 INFO::Creating output folder
2025-09-10 21:10:01.082692 INFO::Creating fits folder
2025-09-10 21:10:01.082992 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de33150d837/fits/residuals_linear.rds
2025-09-10 21:10:01.083414 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de33150d837/fits/fitted_linear.rds
2025-09-10 21:10:01.083771 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de33150d837/fits/residuals_logistic.rds
2025-09-10 21:10:01.084139 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de33150d837/fits/fitted_logistic.rds
2025-09-10 21:10:01.084951 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpfGHQCw/file7de33150d837/all_results.tsv
2025-09-10 21:10:01.08552 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//RtmpfGHQCw/file7de33150d837/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
118.725 5.285 124.660
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.223 | 0.424 | 8.665 | |
| maaslin_check_arguments | 0.060 | 0.002 | 0.061 | |
| maaslin_check_formula | 0.054 | 0.003 | 0.058 | |
| maaslin_compute_formula | 0.059 | 0.003 | 0.061 | |
| maaslin_contrast_test | 7.094 | 0.640 | 7.776 | |
| maaslin_filter | 0.216 | 0.026 | 0.242 | |
| maaslin_fit | 5.233 | 0.564 | 5.877 | |
| maaslin_log_arguments | 0.054 | 0.003 | 0.057 | |
| maaslin_normalize | 0.122 | 0.008 | 0.134 | |
| maaslin_plot_results | 13.550 | 0.675 | 14.254 | |
| maaslin_plot_results_from_output | 13.797 | 0.615 | 14.803 | |
| maaslin_process_metadata | 0.220 | 0.038 | 0.330 | |
| maaslin_read_data | 0.057 | 0.003 | 0.069 | |
| maaslin_reorder_data | 0.058 | 0.004 | 0.071 | |
| maaslin_transform | 0.290 | 0.056 | 0.465 | |
| maaslin_write_results | 5.836 | 0.606 | 6.882 | |
| maaslin_write_results_lefse_format | 5.343 | 0.509 | 5.900 | |
| preprocess_dna_mtx | 0.002 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.000 | 0.001 | |