Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-11 12:07 -0400 (Thu, 11 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4539
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4474
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1150/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: maaslin3
Version: 1.1.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.0.tar.gz
StartedAt: 2025-09-09 08:17:41 -0000 (Tue, 09 Sep 2025)
EndedAt: 2025-09-09 08:32:58 -0000 (Tue, 09 Sep 2025)
EllapsedTime: 917.2 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings maaslin3_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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               52.242  0.207  52.577
maaslin_plot_results_from_output   51.824  0.295  52.239
maaslin3                           29.412  0.582  30.082
maaslin_contrast_test              27.974  0.299  28.360
maaslin_write_results_lefse_format 24.378  0.199  24.647
maaslin_write_results              21.921  0.124  22.100
maaslin_fit                        20.544  0.068  20.659
* 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

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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")
2025-09-09 08:25:47.337358 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:25:47.46338 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:25:47.601716 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:25:47.637449 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:25:47.709641 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:25:47.834068 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:25:47.842446 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:25:47.861732 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:25:48.025239 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:25:48.033463 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:25:48.112266 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:25:48.175686 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:25:48.19444 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:25:48.259425 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:25:48.380903 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:26:10.386579 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:26:10.516473 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:26:10.662425 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:26:10.698104 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:26:10.754491 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:26:10.878589 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:26:10.886902 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:26:10.906052 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:26:11.070474 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:26:11.079337 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:26:11.160791 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:26:11.228343 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:26:11.247887 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:26:11.313545 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:26:11.427822 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:26:35.477473 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:26:35.605682 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:26:35.730786 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:26:35.765818 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:26:35.821667 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:26:35.947836 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:26:35.956571 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:26:35.976087 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:26:36.136643 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:26:36.145302 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:26:37.054236 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:26:37.117457 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:26:37.136234 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:26:37.200446 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:26:37.308732 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:26:56.667075 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:26:56.786173 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:26:56.901263 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:26:56.935663 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:26:56.989256 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:26:57.114087 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:26:57.121964 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:26:57.139906 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:26:57.284136 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:26:57.292168 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:26:57.36737 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:26:57.42812 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:26:57.445891 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:26:57.507065 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:26:57.610731 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:26:57.937598 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/residuals_linear.rds
2025-09-09 08:26:58.005832 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/fitted_linear.rds
2025-09-09 08:26:58.076414 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/residuals_logistic.rds
2025-09-09 08:26:58.421964 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/fitted_logistic.rds
2025-09-09 08:27:19.8429 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:27:19.979394 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:27:20.10337 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:27:20.139313 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:27:20.196005 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:27:20.322505 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:27:20.331301 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:27:20.351024 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:27:20.511435 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:27:20.520976 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:27:20.605686 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:27:20.675975 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:27:20.695255 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:27:20.763126 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:27:20.88364 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:27:41.159842 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:27:41.297217 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:27:41.435352 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:27:41.473264 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:27:41.536115 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:27:41.674847 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:27:41.683511 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:27:41.703174 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:27:41.875693 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:27:41.885106 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:27:41.97894 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:27:42.048554 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:27:42.068922 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:27:42.138227 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:27:42.259663 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:27:42.560519 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/residuals_linear.rds
2025-09-09 08:27:42.622949 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/fitted_linear.rds
2025-09-09 08:27:42.68701 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/residuals_logistic.rds
2025-09-09 08:27:42.982499 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/fitted_logistic.rds
2025-09-09 08:28:04.26377 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:28:04.396929 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:28:04.529419 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:28:04.56793 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:28:04.627859 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:28:04.763003 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:28:04.772113 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:28:04.792881 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:28:04.971388 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:28:04.981426 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:28:05.075868 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:28:05.188684 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:28:05.212759 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:28:05.279643 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:28:05.395275 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:28:25.018754 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:28:25.142975 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:28:25.306845 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:28:25.34688 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:28:25.40572 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:28:25.547861 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:28:25.556518 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:28:25.576123 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:28:25.74451 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:28:25.753825 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:28:25.840395 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:28:25.908819 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:28:25.928369 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:28:25.994311 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:28:26.106792 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:28:26.400957 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/residuals_linear.rds
2025-09-09 08:28:26.467323 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/fitted_linear.rds
2025-09-09 08:28:26.535305 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/residuals_logistic.rds
2025-09-09 08:28:26.868016 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37786285812b/fits/fitted_logistic.rds
2025-09-09 08:28:47.918455 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:28:48.046342 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:28:48.170224 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:28:48.206968 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:28:48.263732 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:28:48.398014 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:28:48.407269 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:28:48.42772 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:28:48.593813 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:28:48.602938 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:28:48.687245 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:28:48.752526 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:28:48.771511 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:28:48.839432 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:28:48.955721 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:29:08.418033 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:29:09.474035 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:29:09.602288 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:29:09.63856 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:29:09.69624 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:29:09.826114 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:29:09.834937 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:29:09.854064 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:29:10.014247 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:29:10.022744 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:29:10.103385 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:29:10.16882 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:29:10.188057 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:29:10.25288 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:29:10.36903 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:29:35.241391 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:29:48.677194 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:30:15.495557 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:30:29.882573 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:30:30.924301 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_linear.rds
2025-09-09 08:30:30.987145 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_linear.rds
2025-09-09 08:30:31.028977 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_logistic.rds
2025-09-09 08:30:31.103539 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_logistic.rds
2025-09-09 08:30:54.220994 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:31:02.14717 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:31:02.631805 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_linear.rds
2025-09-09 08:31:02.693209 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_linear.rds
2025-09-09 08:31:02.733692 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_logistic.rds
2025-09-09 08:31:02.808405 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_logistic.rds
2025-09-09 08:31:22.253419 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:31:30.640324 WARNING::Fitting problem for feature 124 returning NA
2025-09-09 08:31:31.196042 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_linear.rds
2025-09-09 08:31:31.266756 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_linear.rds
2025-09-09 08:31:31.311689 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_logistic.rds
2025-09-09 08:31:31.392933 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_logistic.rds
2025-09-09 08:31:51.947386 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:31:52.078405 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:31:52.208637 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:31:52.245143 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:31:52.304778 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:31:52.440198 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:31:52.449257 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:31:52.470247 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:31:52.644633 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:31:52.654205 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:31:52.748411 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:31:52.820461 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:31:52.840958 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:31:52.911559 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:31:53.032105 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:32:12.701406 WARNING::Fitting problem for feature 50 returning NA
2025-09-09 08:32:12.83365 WARNING::Fitting problem for feature 62 returning NA
2025-09-09 08:32:12.96055 WARNING::Fitting problem for feature 74 returning NA
2025-09-09 08:32:12.999299 WARNING::Fitting problem for feature 78 returning NA
2025-09-09 08:32:13.059271 WARNING::Fitting problem for feature 84 returning NA
2025-09-09 08:32:13.192444 WARNING::Fitting problem for feature 96 returning NA
2025-09-09 08:32:13.20216 WARNING::Fitting problem for feature 97 returning NA
2025-09-09 08:32:13.224327 WARNING::Fitting problem for feature 99 returning NA
2025-09-09 08:32:13.401861 WARNING::Fitting problem for feature 114 returning NA
2025-09-09 08:32:13.411539 WARNING::Fitting problem for feature 115 returning NA
2025-09-09 08:32:13.498101 WARNING::Fitting problem for feature 123 returning NA
2025-09-09 08:32:13.567311 WARNING::Fitting problem for feature 130 returning NA
2025-09-09 08:32:13.587416 WARNING::Fitting problem for feature 132 returning NA
2025-09-09 08:32:13.656802 WARNING::Fitting problem for feature 139 returning NA
2025-09-09 08:32:13.770785 WARNING::Fitting problem for feature 150 returning NA
2025-09-09 08:32:14.169628 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_linear.rds
2025-09-09 08:32:14.239391 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_linear.rds
2025-09-09 08:32:14.31058 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/residuals_logistic.rds
2025-09-09 08:32:14.663846 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpfLttDH/file1b37785373d3b7/fits/fitted_logistic.rds
2025-09-09 08:32:35.482103 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-09 08:32:35.510451 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-09 08:32:35.529486 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-09 08:32:35.614128 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-09-09 08:32:35.641273 ERROR::Effect name not found in metadata: d
2025-09-09 08:32:35.660564 ERROR::No user formula provided
2025-09-09 08:32:35.705129 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-09 08:32:35.722802 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-09-09 08:32:40.740709 INFO::Writing function arguments to log file
2025-09-09 08:32:40.76315 INFO::Verifying options selected are valid
2025-09-09 08:32:43.30543 INFO::Writing function arguments to log file
2025-09-09 08:32:43.323868 INFO::Verifying options selected are valid
2025-09-09 08:32:43.325484 INFO::Determining format of input files
2025-09-09 08:32:43.326967 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 08:32:43.330476 INFO::Running selected normalization method: TSS
2025-09-09 08:32:43.3327 INFO::Creating output feature tables folder
2025-09-09 08:32:43.334327 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/features/data_norm.tsv
2025-09-09 08:32:43.336498 INFO::Filter data based on min abundance and min prevalence
2025-09-09 08:32:43.337971 INFO::Total samples in data: 16
2025-09-09 08:32:43.339353 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-09 08:32:43.342284 INFO::Total filtered features: 0
2025-09-09 08:32:43.343892 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-09 08:32:43.345731 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-09 08:32:43.347345 INFO::Filtered feature names from variance filtering:
2025-09-09 08:32:43.348792 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/features/filtered_data.tsv
2025-09-09 08:32:43.351069 INFO::Running selected transform method: LOG
2025-09-09 08:32:43.352998 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/features/data_transformed.tsv
2025-09-09 08:32:43.355595 INFO::Applying z-score to standardize continuous metadata
2025-09-09 08:32:43.363813 INFO::Running the linear model component
2025-09-09 08:32:43.386164 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:43.393203 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:43.400527 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:43.413012 INFO::Counting total values for each feature
2025-09-09 08:32:43.416205 INFO::Running the logistic model component
2025-09-09 08:32:43.438726 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:43.448856 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:43.459356 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:43.473554 INFO::Counting total values for each feature
2025-09-09 08:32:43.476997 INFO::Re-running abundances for warn_prevalence
2025-09-09 08:32:43.478489 INFO::Running selected normalization method: TSS
2025-09-09 08:32:43.480713 INFO::Running selected transform method: LOG
2025-09-09 08:32:43.50217 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:43.508829 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:43.515441 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:43.661098 INFO::Creating fits folder
2025-09-09 08:32:43.663084 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/fits/residuals_linear.rds
2025-09-09 08:32:43.664887 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/fits/fitted_linear.rds
2025-09-09 08:32:43.66709 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/fits/residuals_logistic.rds
2025-09-09 08:32:43.669211 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/fits/fitted_logistic.rds
2025-09-09 08:32:43.674106 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/all_results.tsv
2025-09-09 08:32:43.677174 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): /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/significant_results.tsv
2025-09-09 08:32:43.679688 INFO::Creating output figures folder
2025-09-09 08:32:43.681968 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/figures/summary_plot.pdf
2025-09-09 08:32:45.568626 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/figures
2025-09-09 08:32:45.57227 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-09 08:32:45.581717 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-09 08:32:46.144387 INFO::Writing summary plot of
                        significant results to file: /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/figures/summary_plot.pdf
2025-09-09 08:32:48.089237 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpfLttDH/file1b377838382d4a/figures
2025-09-09 08:32:48.09206 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-09 08:32:48.10088 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-09 08:32:48.676364 INFO::Running the linear model component
2025-09-09 08:32:48.693496 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:48.701734 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:48.709671 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:48.723367 INFO::Counting total values for each feature
2025-09-09 08:32:48.726413 INFO::Running the logistic model component
2025-09-09 08:32:48.742745 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:48.75407 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:48.765101 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:48.782359 INFO::Counting total values for each feature
2025-09-09 08:32:48.786244 INFO::Re-running abundances for warn_prevalence
2025-09-09 08:32:48.787755 INFO::Running selected normalization method: TSS
2025-09-09 08:32:48.790475 INFO::Running selected transform method: LOG
2025-09-09 08:32:48.808188 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:48.816413 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:48.824632 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:48.981988 INFO::Creating output folder
2025-09-09 08:32:48.983625 INFO::Creating output figures folder
2025-09-09 08:32:48.985768 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpfLttDH/file1b37784f0f4dd1/figures/summary_plot.pdf
2025-09-09 08:32:50.888499 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpfLttDH/file1b37784f0f4dd1/figures
2025-09-09 08:32:50.891645 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-09 08:32:50.900219 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-09 08:32:52.245567 INFO::Applying z-score to standardize continuous metadata
2025-09-09 08:32:52.258955 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-09 08:32:52.260316 INFO::Bypass z-score application to metadata
2025-09-09 08:32:52.264626 INFO::Bypass z-score application to metadata
2025-09-09 08:32:52.29564 INFO::Determining format of input files
2025-09-09 08:32:52.297225 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 08:32:52.298803 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-09 08:32:52.311389 INFO::Determining format of input files
2025-09-09 08:32:52.31325 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-09 08:32:52.315652 INFO::Input format is feature_specific_covariate samples as columns
2025-09-09 08:32:52.330582 INFO::Determining format of input files
2025-09-09 08:32:52.332474 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-09 08:32:52.334587 INFO::Input format is feature_specific_covariate samples as columns
2025-09-09 08:32:52.337731 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-09 08:32:52.339274 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-09 08:32:52.357961 INFO::Running selected transform method: LOG
2025-09-09 08:32:52.359855 INFO::Creating output feature tables folder
2025-09-09 08:32:52.361427 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783ef1e778/features/data_transformed.tsv
2025-09-09 08:32:52.368194 INFO::Running selected transform method: LOG
2025-09-09 08:32:52.370186 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783ef1e778/features/data_transformed.tsv
2025-09-09 08:32:52.379709 INFO::Running selected transform method: PLOG
2025-09-09 08:32:52.382883 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783ef1e778/features/data_transformed.tsv
2025-09-09 08:32:52.38806 INFO::Running selected transform method: NONE
2025-09-09 08:32:52.38962 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783ef1e778/features/data_transformed.tsv
2025-09-09 08:32:52.401432 INFO::Running the linear model component
2025-09-09 08:32:52.417744 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:52.425564 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:52.432977 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:52.445575 INFO::Counting total values for each feature
2025-09-09 08:32:52.448504 INFO::Running the logistic model component
2025-09-09 08:32:52.463946 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:52.474857 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:52.485541 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:52.500947 INFO::Counting total values for each feature
2025-09-09 08:32:52.504528 INFO::Re-running abundances for warn_prevalence
2025-09-09 08:32:52.506094 INFO::Running selected normalization method: TSS
2025-09-09 08:32:52.508694 INFO::Running selected transform method: LOG
2025-09-09 08:32:52.52534 INFO::Fitting model to feature number 1, a
2025-09-09 08:32:52.53321 INFO::Fitting model to feature number 2, b
2025-09-09 08:32:52.541313 INFO::Fitting model to feature number 3, c
2025-09-09 08:32:52.704483 INFO::Creating output folder
2025-09-09 08:32:52.706371 INFO::Creating fits folder
2025-09-09 08:32:52.708071 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783d92e921/fits/residuals_linear.rds
2025-09-09 08:32:52.709881 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783d92e921/fits/fitted_linear.rds
2025-09-09 08:32:52.711905 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783d92e921/fits/residuals_logistic.rds
2025-09-09 08:32:52.713807 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpfLttDH/file1b37783d92e921/fits/fitted_logistic.rds
2025-09-09 08:32:52.718149 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpfLttDH/file1b37783d92e921/all_results.tsv
2025-09-09 08:32:52.720648 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): /home/biocbuild/tmp/RtmpfLttDH/file1b37783d92e921/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
433.703   4.629 439.413

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin329.412 0.58230.082
maaslin_check_arguments0.1810.0000.182
maaslin_check_formula0.1990.0000.200
maaslin_compute_formula0.2080.0000.209
maaslin_contrast_test27.974 0.29928.360
maaslin_filter1.3790.0601.443
maaslin_fit20.544 0.06820.659
maaslin_log_arguments0.1980.0000.198
maaslin_normalize0.3730.0000.373
maaslin_plot_results52.242 0.20752.577
maaslin_plot_results_from_output51.824 0.29552.239
maaslin_process_metadata0.6650.0080.674
maaslin_read_data0.1980.0000.198
maaslin_reorder_data0.2110.0040.215
maaslin_transform0.7760.0200.799
maaslin_write_results21.921 0.12422.100
maaslin_write_results_lefse_format24.378 0.19924.647
preprocess_dna_mtx0.0060.0000.005
preprocess_taxa_mtx0.0060.0000.006