Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 1155/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.0.0  (landing page)
William Nickols
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: RELEASE_3_21
git_last_commit: 7584c46
git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for maaslin3 on kunpeng2

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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2025-09-23 11:26:59 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 11:43:47 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 1008.4 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.0.0’
* 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               54.297  0.310  55.557
maaslin_plot_results_from_output   53.292  0.331  55.645
maaslin3                           31.007  0.442  31.628
maaslin_contrast_test              31.014  0.200  31.317
maaslin_write_results_lefse_format 25.498  0.135  26.537
maaslin_write_results              24.148  0.163  24.940
maaslin_fit                        22.621  0.044  22.726
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.0.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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")
2025-09-23 11:35:51.155366 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:35:51.291858 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:35:51.43994 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:35:51.478583 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:35:51.556012 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:35:51.695888 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:35:51.705066 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:35:51.72633 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:35:51.914286 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:35:51.923937 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:35:52.020335 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:35:52.092254 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:35:52.113185 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:35:52.185627 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:35:52.319534 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:36:18.529294 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:36:18.665638 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:36:18.798544 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:36:18.837667 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:36:18.901547 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:36:19.041962 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:36:19.051139 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:36:19.072184 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:36:19.253017 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:36:19.262817 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:36:19.375845 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:36:19.445168 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:36:19.465411 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:36:19.583309 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:36:19.704964 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:36:44.667624 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:36:44.879669 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:36:45.014925 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:36:45.054099 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:36:45.117643 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:36:45.257284 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:36:45.266638 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:36:45.288022 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:36:45.464426 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:36:45.474106 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:36:45.564355 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:36:46.740655 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:36:46.76104 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:36:46.83152 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:36:46.951755 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:37:09.679063 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:37:09.872371 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:37:10.001132 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:37:10.037856 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:37:10.097296 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:37:10.229511 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:37:10.238139 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:37:10.258028 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:37:10.44046 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:37:10.44936 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:37:10.527906 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:37:10.594506 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:37:10.615877 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:37:10.689383 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:37:10.846963 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:37:11.216026 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/residuals_linear.rds
2025-09-23 11:37:11.284894 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/fitted_linear.rds
2025-09-23 11:37:11.35576 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/residuals_logistic.rds
2025-09-23 11:37:11.701342 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/fitted_logistic.rds
2025-09-23 11:37:34.227571 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:37:34.361223 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:37:34.491607 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:37:34.529341 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:37:34.587529 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:37:34.716826 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:37:34.725456 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:37:34.746228 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:37:34.910099 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:37:34.919233 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:37:35.00546 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:37:35.074342 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:37:35.115054 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:37:35.264766 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:37:35.422137 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:37:58.40176 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:37:58.534964 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:37:59.921226 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:37:59.957906 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:38:00.017115 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:38:00.152366 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:38:00.161096 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:38:00.181385 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:38:00.346541 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:38:00.355563 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:38:00.444443 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:38:00.514733 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:38:00.535115 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:38:00.607323 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:38:00.733986 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:38:01.061896 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/residuals_linear.rds
2025-09-23 11:38:01.130719 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/fitted_linear.rds
2025-09-23 11:38:01.201362 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/residuals_logistic.rds
2025-09-23 11:38:01.546244 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/fitted_logistic.rds
2025-09-23 11:38:24.647547 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:38:24.792066 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:38:24.929996 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:38:24.969447 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:38:25.032934 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:38:25.169307 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:38:25.178385 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:38:25.199331 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:38:25.370701 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:38:25.379951 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:38:25.468292 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:38:25.540395 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:38:25.5621 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:38:25.633326 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:38:25.75627 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:38:49.22848 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:38:49.360149 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:38:49.490432 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:38:49.528076 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:38:49.587093 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:38:49.717286 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:38:49.72603 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:38:49.745991 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:38:49.919042 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:38:49.927681 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:38:50.00914 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:38:50.076489 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:38:50.096322 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:38:50.161834 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:38:50.273204 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:38:50.57555 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/residuals_linear.rds
2025-09-23 11:38:50.644782 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/fitted_linear.rds
2025-09-23 11:38:50.724041 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/residuals_logistic.rds
2025-09-23 11:38:51.448285 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984edbf4864/fits/fitted_logistic.rds
2025-09-23 11:39:14.461485 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:39:14.614329 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:39:14.764586 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:39:14.80656 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:39:14.871843 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:39:15.015019 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:39:15.024674 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:39:15.046378 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:39:15.225079 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:39:15.234809 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:39:15.329647 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:39:15.405576 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:39:15.427516 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:39:15.503687 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:39:15.633775 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:39:37.445371 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:39:37.575638 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:39:37.749111 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:39:37.788817 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:39:37.849921 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:39:37.989489 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:39:37.998333 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:39:38.018534 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:39:38.183669 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:39:38.192593 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:39:38.276904 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:39:38.346352 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:39:38.366338 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:39:38.434778 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:39:38.551923 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:40:05.779724 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:40:23.365089 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:40:51.51135 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:41:08.216084 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:41:09.248624 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_linear.rds
2025-09-23 11:41:09.319944 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_linear.rds
2025-09-23 11:41:09.364842 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_logistic.rds
2025-09-23 11:41:09.44709 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_logistic.rds
2025-09-23 11:41:34.16076 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:41:43.200457 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:41:43.934471 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_linear.rds
2025-09-23 11:41:43.997515 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_linear.rds
2025-09-23 11:41:44.040244 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_logistic.rds
2025-09-23 11:41:44.118785 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_logistic.rds
2025-09-23 11:42:06.02725 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:42:15.860494 WARNING::Fitting problem for feature 124 returning NA
2025-09-23 11:42:16.458186 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_linear.rds
2025-09-23 11:42:16.519921 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_linear.rds
2025-09-23 11:42:16.561726 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_logistic.rds
2025-09-23 11:42:16.639293 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_logistic.rds
2025-09-23 11:42:37.262825 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:42:37.410928 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:42:37.557373 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:42:37.601366 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:42:37.672081 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:42:37.813811 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:42:37.823008 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:42:37.843657 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:42:38.013892 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:42:38.023087 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:42:38.110513 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:42:38.181258 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:42:38.201947 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:42:38.273566 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:42:38.39823 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:43:00.530069 WARNING::Fitting problem for feature 50 returning NA
2025-09-23 11:43:00.67013 WARNING::Fitting problem for feature 62 returning NA
2025-09-23 11:43:00.823579 WARNING::Fitting problem for feature 74 returning NA
2025-09-23 11:43:00.860792 WARNING::Fitting problem for feature 78 returning NA
2025-09-23 11:43:00.918644 WARNING::Fitting problem for feature 84 returning NA
2025-09-23 11:43:01.050148 WARNING::Fitting problem for feature 96 returning NA
2025-09-23 11:43:01.059245 WARNING::Fitting problem for feature 97 returning NA
2025-09-23 11:43:01.080977 WARNING::Fitting problem for feature 99 returning NA
2025-09-23 11:43:01.248299 WARNING::Fitting problem for feature 114 returning NA
2025-09-23 11:43:01.257324 WARNING::Fitting problem for feature 115 returning NA
2025-09-23 11:43:01.343744 WARNING::Fitting problem for feature 123 returning NA
2025-09-23 11:43:01.410909 WARNING::Fitting problem for feature 130 returning NA
2025-09-23 11:43:01.431211 WARNING::Fitting problem for feature 132 returning NA
2025-09-23 11:43:01.503514 WARNING::Fitting problem for feature 139 returning NA
2025-09-23 11:43:01.621712 WARNING::Fitting problem for feature 150 returning NA
2025-09-23 11:43:02.033668 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_linear.rds
2025-09-23 11:43:02.102822 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_linear.rds
2025-09-23 11:43:02.246856 WARNING::Deleting existing residuals file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/residuals_logistic.rds
2025-09-23 11:43:02.958251 WARNING::Deleting existing fitted file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e2bbfe17c/fits/fitted_logistic.rds
2025-09-23 11:43:23.588808 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-23 11:43:23.618799 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-23 11:43:23.658513 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-23 11:43:23.833918 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-09-23 11:43:23.883965 ERROR::Effect name not found in metadata: d
2025-09-23 11:43:23.922445 ERROR::No user formula provided
2025-09-23 11:43:23.969501 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-23 11:43:23.988605 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-09-23 11:43:29.253389 INFO::Writing function arguments to log file
2025-09-23 11:43:29.274794 INFO::Verifying options selected are valid
2025-09-23 11:43:31.890057 INFO::Writing function arguments to log file
2025-09-23 11:43:31.908845 INFO::Verifying options selected are valid
2025-09-23 11:43:31.910423 INFO::Determining format of input files
2025-09-23 11:43:31.911899 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-23 11:43:31.915552 INFO::Running selected normalization method: TSS
2025-09-23 11:43:31.917881 INFO::Creating output feature tables folder
2025-09-23 11:43:31.919418 INFO::Writing normalized data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/features/data_norm.tsv
2025-09-23 11:43:31.921731 INFO::Filter data based on min abundance and min prevalence
2025-09-23 11:43:31.923187 INFO::Total samples in data: 16
2025-09-23 11:43:31.924614 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-23 11:43:31.927509 INFO::Total filtered features: 0
2025-09-23 11:43:31.929146 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-23 11:43:31.930995 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-23 11:43:31.932566 INFO::Filtered feature names from variance filtering:
2025-09-23 11:43:31.93402 INFO::Writing filtered data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/features/filtered_data.tsv
2025-09-23 11:43:31.936307 INFO::Running selected transform method: LOG
2025-09-23 11:43:31.938234 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/features/data_transformed.tsv
2025-09-23 11:43:31.940847 INFO::Applying z-score to standardize continuous metadata
2025-09-23 11:43:31.948653 INFO::Running the linear model component
2025-09-23 11:43:31.970439 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:31.977281 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:31.984425 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:31.995798 INFO::Counting total values for each feature
2025-09-23 11:43:31.998827 INFO::Running the logistic model component
2025-09-23 11:43:32.020931 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:32.031054 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:32.043058 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:32.057559 INFO::Counting total values for each feature
2025-09-23 11:43:32.061082 INFO::Re-running abundances for warn_prevalence
2025-09-23 11:43:32.062706 INFO::Running selected normalization method: TSS
2025-09-23 11:43:32.065165 INFO::Running selected transform method: LOG
2025-09-23 11:43:32.086865 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:32.09357 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:32.100308 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:32.240958 INFO::Creating fits folder
2025-09-23 11:43:32.242806 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/fits/residuals_linear.rds
2025-09-23 11:43:32.244625 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/fits/fitted_linear.rds
2025-09-23 11:43:32.246669 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/fits/residuals_logistic.rds
2025-09-23 11:43:32.248728 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/fits/fitted_logistic.rds
2025-09-23 11:43:32.253162 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/all_results.tsv
2025-09-23 11:43:32.255844 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/RtmpWJMOjS/file35984e1e1e9ffd/significant_results.tsv
2025-09-23 11:43:32.258139 INFO::Creating output figures folder
2025-09-23 11:43:32.260441 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/figures/summary_plot.pdf
2025-09-23 11:43:34.001495 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/figures
2025-09-23 11:43:34.004398 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-23 11:43:34.011989 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-23 11:43:34.531679 INFO::Writing summary plot of
                        significant results to file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/figures/summary_plot.pdf
2025-09-23 11:43:36.452253 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpWJMOjS/file35984e1e1e9ffd/figures
2025-09-23 11:43:36.45448 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-23 11:43:36.461565 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-23 11:43:36.973728 INFO::Running the linear model component
2025-09-23 11:43:36.987415 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:36.993774 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:36.999822 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:37.01004 INFO::Counting total values for each feature
2025-09-23 11:43:37.012657 INFO::Running the logistic model component
2025-09-23 11:43:37.026032 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:37.035153 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:37.044202 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:37.057387 INFO::Counting total values for each feature
2025-09-23 11:43:37.060596 INFO::Re-running abundances for warn_prevalence
2025-09-23 11:43:37.061822 INFO::Running selected normalization method: TSS
2025-09-23 11:43:37.063831 INFO::Running selected transform method: LOG
2025-09-23 11:43:37.07751 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:37.083736 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:37.089798 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:37.221934 INFO::Creating output folder
2025-09-23 11:43:37.223367 INFO::Creating output figures folder
2025-09-23 11:43:37.225298 INFO::Writing summary plot of significant
                        results to file: /home/biocbuild/tmp/RtmpWJMOjS/file35984e4a26275/figures/summary_plot.pdf
2025-09-23 11:43:38.976684 INFO::Writing association plots (one for each significant association) to output folder: /home/biocbuild/tmp/RtmpWJMOjS/file35984e4a26275/figures
2025-09-23 11:43:38.979232 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-23 11:43:38.986604 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-23 11:43:40.329053 INFO::Applying z-score to standardize continuous metadata
2025-09-23 11:43:40.340678 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-23 11:43:40.341958 INFO::Bypass z-score application to metadata
2025-09-23 11:43:40.345828 INFO::Bypass z-score application to metadata
2025-09-23 11:43:40.372124 INFO::Determining format of input files
2025-09-23 11:43:40.373538 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-23 11:43:40.374795 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-23 11:43:40.385856 INFO::Determining format of input files
2025-09-23 11:43:40.387516 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-23 11:43:40.389562 INFO::Input format is feature_specific_covariate samples as columns
2025-09-23 11:43:40.401729 INFO::Determining format of input files
2025-09-23 11:43:40.403224 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-23 11:43:40.404827 INFO::Input format is feature_specific_covariate samples as columns
2025-09-23 11:43:40.407383 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-23 11:43:40.408617 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-23 11:43:40.424968 INFO::Running selected transform method: LOG
2025-09-23 11:43:40.426582 INFO::Creating output feature tables folder
2025-09-23 11:43:40.42784 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e59e61d86/features/data_transformed.tsv
2025-09-23 11:43:40.43366 INFO::Running selected transform method: LOG
2025-09-23 11:43:40.435319 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e59e61d86/features/data_transformed.tsv
2025-09-23 11:43:40.441086 INFO::Running selected transform method: PLOG
2025-09-23 11:43:40.443628 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e59e61d86/features/data_transformed.tsv
2025-09-23 11:43:40.44786 INFO::Running selected transform method: NONE
2025-09-23 11:43:40.449494 INFO::Writing normalized, filtered, transformed data to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e59e61d86/features/data_transformed.tsv
2025-09-23 11:43:40.465665 INFO::Running the linear model component
2025-09-23 11:43:40.479465 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:40.485834 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:40.491879 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:40.502202 INFO::Counting total values for each feature
2025-09-23 11:43:40.504741 INFO::Running the logistic model component
2025-09-23 11:43:40.519526 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:40.528816 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:40.537673 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:40.550558 INFO::Counting total values for each feature
2025-09-23 11:43:40.553697 INFO::Re-running abundances for warn_prevalence
2025-09-23 11:43:40.554836 INFO::Running selected normalization method: TSS
2025-09-23 11:43:40.556849 INFO::Running selected transform method: LOG
2025-09-23 11:43:40.570436 INFO::Fitting model to feature number 1, a
2025-09-23 11:43:40.576773 INFO::Fitting model to feature number 2, b
2025-09-23 11:43:40.582858 INFO::Fitting model to feature number 3, c
2025-09-23 11:43:40.720047 INFO::Creating output folder
2025-09-23 11:43:40.721504 INFO::Creating fits folder
2025-09-23 11:43:40.722723 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1fcff925/fits/residuals_linear.rds
2025-09-23 11:43:40.72411 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1fcff925/fits/fitted_linear.rds
2025-09-23 11:43:40.725706 INFO::Writing residuals to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1fcff925/fits/residuals_logistic.rds
2025-09-23 11:43:40.727087 INFO::Writing fitted values to file /home/biocbuild/tmp/RtmpWJMOjS/file35984e1fcff925/fits/fitted_logistic.rds
2025-09-23 11:43:40.730708 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /home/biocbuild/tmp/RtmpWJMOjS/file35984e1fcff925/all_results.tsv
2025-09-23 11:43:40.73287 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/RtmpWJMOjS/file35984e1fcff925/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
463.824   4.596 486.726

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin331.007 0.44231.628
maaslin_check_arguments0.2130.0000.213
maaslin_check_formula0.2070.0080.216
maaslin_compute_formula0.2150.0040.220
maaslin_contrast_test31.014 0.20031.317
maaslin_filter0.6440.0120.658
maaslin_fit22.621 0.04422.726
maaslin_log_arguments0.2050.0000.205
maaslin_normalize0.4020.0000.403
maaslin_plot_results54.297 0.31055.557
maaslin_plot_results_from_output53.292 0.33155.645
maaslin_process_metadata0.7040.0080.714
maaslin_read_data0.2150.0000.216
maaslin_reorder_data0.2180.0120.267
maaslin_transform0.8460.0310.880
maaslin_write_results24.148 0.16324.940
maaslin_write_results_lefse_format25.498 0.13526.537
preprocess_dna_mtx0.0050.0000.005
preprocess_taxa_mtx0.0020.0030.006