Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-28 11:40 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-25 13:40 -0400 (Mon, 25 Aug 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    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for maaslin3 on merida1

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.

raw results


Summary

Package: maaslin3
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2025-08-26 05:35:01 -0400 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 05:59:59 -0400 (Tue, 26 Aug 2025)
EllapsedTime: 1498.4 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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               82.518  1.796  88.763
maaslin_plot_results_from_output   81.522  1.347  87.599
maaslin_contrast_test              43.329  1.798  48.218
maaslin3                           40.897  1.538  45.354
maaslin_write_results_lefse_format 37.420  0.789  40.762
maaslin_write_results              32.921  0.968  36.221
maaslin_fit                        31.424  1.002  36.928
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-08-26 05:48:22.068718 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:48:22.291065 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:48:22.51979 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:48:22.58955 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:48:22.687043 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:48:22.899184 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:48:22.913596 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:48:22.945866 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:48:23.215855 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:48:23.229697 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:48:23.367581 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:48:23.510119 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:48:23.541901 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:48:23.649719 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:48:23.833238 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:48:58.505649 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:48:58.789442 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:48:59.017451 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:48:59.103134 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:48:59.199111 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:48:59.466955 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:48:59.484278 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:48:59.523987 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:48:59.816588 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:48:59.831316 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:48:59.966857 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:49:00.077536 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:49:00.109362 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:49:00.223889 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:49:00.419057 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:49:08.149 R[48642:342563366] XType: com.apple.fonts is not accessible.
2025-08-26 05:49:08.150 R[48642:342563366] XType: XTFontStaticRegistry is enabled.
2025-08-26 05:49:42.458129 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:49:42.6684 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:49:42.867251 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:49:42.931886 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:49:43.031617 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:49:43.244557 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:49:43.291347 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:49:43.323842 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:49:43.606946 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:49:43.621436 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:49:43.808168 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:49:43.916839 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:49:43.946833 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:49:44.049892 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:49:44.230341 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:50:14.292216 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:50:14.512326 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:50:14.728831 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:50:14.791818 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:50:14.88604 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:50:15.104933 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:50:15.119404 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:50:15.153088 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:50:15.48143 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:50:15.498169 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:50:15.643424 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:50:15.765111 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:50:15.799224 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:50:15.913316 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:50:16.111637 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:50:16.657174 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/residuals_linear.rds
2025-08-26 05:50:16.762592 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/fitted_linear.rds
2025-08-26 05:50:16.875581 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/residuals_logistic.rds
2025-08-26 05:50:17.513106 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/fitted_logistic.rds
2025-08-26 05:50:55.263939 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:50:55.510862 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:50:55.752581 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:50:55.82912 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:50:55.92771 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:50:56.135847 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:50:56.151294 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:50:56.183157 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:50:56.544936 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:50:56.575884 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:50:56.729034 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:50:56.849846 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:50:56.884875 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:50:57.073643 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:50:57.283111 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:51:27.555556 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:51:27.762783 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:51:27.967305 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:51:28.032002 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:51:28.128847 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:51:28.341712 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:51:28.355756 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:51:28.389493 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:51:28.652012 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:51:28.666797 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:51:28.808214 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:51:28.924917 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:51:28.960899 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:51:29.079843 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:51:29.279237 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:51:29.814897 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/residuals_linear.rds
2025-08-26 05:51:29.92436 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/fitted_linear.rds
2025-08-26 05:51:30.037215 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/residuals_logistic.rds
2025-08-26 05:51:30.63702 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/fitted_logistic.rds
2025-08-26 05:52:07.497571 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:52:07.714712 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:52:07.933068 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:52:07.99594 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:52:08.095859 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:52:08.313857 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:52:08.326506 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:52:08.354672 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:52:08.692274 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:52:08.707768 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:52:08.852912 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:52:08.953392 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:52:08.9846 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:52:09.095694 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:52:09.288623 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:52:37.877118 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:52:38.085385 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:52:38.289101 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:52:38.349031 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:52:38.440907 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:52:38.685266 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:52:38.69927 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:52:38.72992 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:52:38.988391 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:52:39.003052 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:52:39.142202 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:52:39.251079 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:52:39.282705 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:52:39.423316 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:52:39.722711 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:52:40.256418 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/residuals_linear.rds
2025-08-26 05:52:40.370147 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/fitted_linear.rds
2025-08-26 05:52:40.481255 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/residuals_logistic.rds
2025-08-26 05:52:41.116508 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02334c76af/fits/fitted_logistic.rds
2025-08-26 05:53:15.999271 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:53:16.202801 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:53:16.406968 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:53:16.465136 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:53:16.555938 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:53:16.759218 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:53:16.772579 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:53:16.805536 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:53:17.053613 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:53:17.067773 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:53:17.251614 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:53:17.357643 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:53:17.388402 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:53:17.494843 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:53:17.686836 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:53:45.902472 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:53:46.151807 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:53:46.362061 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:53:46.420689 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:53:46.697098 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:53:46.895064 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:53:46.908794 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:53:46.939368 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:53:47.182499 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:53:47.196855 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:53:47.332789 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:53:47.437989 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:53:47.476957 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:53:47.585804 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:53:47.770379 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:54:28.547721 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:54:48.331841 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:55:32.600412 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:55:52.061816 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:55:53.617786 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_linear.rds
2025-08-26 05:55:53.727141 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_linear.rds
2025-08-26 05:55:53.793264 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_logistic.rds
2025-08-26 05:55:53.927588 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_logistic.rds
2025-08-26 05:56:33.548044 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:56:46.249768 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:56:47.037584 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_linear.rds
2025-08-26 05:56:47.141313 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_linear.rds
2025-08-26 05:56:47.225411 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_logistic.rds
2025-08-26 05:56:47.363162 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_logistic.rds
2025-08-26 05:57:20.228146 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:57:32.58126 WARNING::Fitting problem for feature 124 returning NA
2025-08-26 05:57:33.378907 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_linear.rds
2025-08-26 05:57:33.483644 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_linear.rds
2025-08-26 05:57:33.555536 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_logistic.rds
2025-08-26 05:57:33.687327 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_logistic.rds
2025-08-26 05:58:04.514807 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:58:04.692611 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:58:04.884379 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:58:04.945569 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:58:05.035784 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:58:05.240359 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:58:05.254733 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:58:05.288176 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:58:05.544662 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:58:05.56119 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:58:05.694221 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:58:05.811392 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:58:05.845305 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:58:05.954799 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:58:06.197752 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:58:34.557539 WARNING::Fitting problem for feature 50 returning NA
2025-08-26 05:58:34.764906 WARNING::Fitting problem for feature 62 returning NA
2025-08-26 05:58:34.974428 WARNING::Fitting problem for feature 74 returning NA
2025-08-26 05:58:35.035516 WARNING::Fitting problem for feature 78 returning NA
2025-08-26 05:58:35.132245 WARNING::Fitting problem for feature 84 returning NA
2025-08-26 05:58:35.346385 WARNING::Fitting problem for feature 96 returning NA
2025-08-26 05:58:35.361106 WARNING::Fitting problem for feature 97 returning NA
2025-08-26 05:58:35.394786 WARNING::Fitting problem for feature 99 returning NA
2025-08-26 05:58:35.667086 WARNING::Fitting problem for feature 114 returning NA
2025-08-26 05:58:35.681902 WARNING::Fitting problem for feature 115 returning NA
2025-08-26 05:58:35.828019 WARNING::Fitting problem for feature 123 returning NA
2025-08-26 05:58:35.949247 WARNING::Fitting problem for feature 130 returning NA
2025-08-26 05:58:35.9836 WARNING::Fitting problem for feature 132 returning NA
2025-08-26 05:58:36.106043 WARNING::Fitting problem for feature 139 returning NA
2025-08-26 05:58:36.313619 WARNING::Fitting problem for feature 150 returning NA
2025-08-26 05:58:37.093047 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_linear.rds
2025-08-26 05:58:37.20453 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_linear.rds
2025-08-26 05:58:37.315359 WARNING::Deleting existing residuals file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/residuals_logistic.rds
2025-08-26 05:58:37.90637 WARNING::Deleting existing fitted file: /tmp/Rtmp3XwaYS/filebe02202e0574/fits/fitted_logistic.rds
2025-08-26 05:59:11.583787 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-26 05:59:11.629304 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-26 05:59:11.659523 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-26 05:59:11.798537 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-26 05:59:11.840843 ERROR::Effect name not found in metadata: d
2025-08-26 05:59:11.870086 ERROR::No user formula provided
2025-08-26 05:59:11.946493 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-26 05:59:11.977105 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-26 05:59:21.63872 INFO::Writing function arguments to log file
2025-08-26 05:59:21.680036 INFO::Verifying options selected are valid
2025-08-26 05:59:25.96677 INFO::Writing function arguments to log file
2025-08-26 05:59:26.001456 INFO::Verifying options selected are valid
2025-08-26 05:59:26.004299 INFO::Determining format of input files
2025-08-26 05:59:26.00723 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-26 05:59:26.014074 INFO::Running selected normalization method: TSS
2025-08-26 05:59:26.018097 INFO::Creating output feature tables folder
2025-08-26 05:59:26.021153 INFO::Writing normalized data to file /tmp/Rtmp3XwaYS/filebe021a03c846/features/data_norm.tsv
2025-08-26 05:59:26.025426 INFO::Filter data based on min abundance and min prevalence
2025-08-26 05:59:26.027824 INFO::Total samples in data: 16
2025-08-26 05:59:26.030046 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-26 05:59:26.034539 INFO::Total filtered features: 0
2025-08-26 05:59:26.037636 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-26 05:59:26.040919 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-26 05:59:26.043742 INFO::Filtered feature names from variance filtering:
2025-08-26 05:59:26.04642 INFO::Writing filtered data to file /tmp/Rtmp3XwaYS/filebe021a03c846/features/filtered_data.tsv
2025-08-26 05:59:26.051185 INFO::Running selected transform method: LOG
2025-08-26 05:59:26.054687 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3XwaYS/filebe021a03c846/features/data_transformed.tsv
2025-08-26 05:59:26.059788 INFO::Applying z-score to standardize continuous metadata
2025-08-26 05:59:26.07186 INFO::Running the linear model component
2025-08-26 05:59:26.118418 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:26.129861 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:26.141114 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:26.156892 INFO::Counting total values for each feature
2025-08-26 05:59:26.161463 INFO::Running the logistic model component
2025-08-26 05:59:26.200844 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:26.215982 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:26.232527 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:26.255518 INFO::Counting total values for each feature
2025-08-26 05:59:26.261248 INFO::Re-running abundances for warn_prevalence
2025-08-26 05:59:26.264066 INFO::Running selected normalization method: TSS
2025-08-26 05:59:26.268245 INFO::Running selected transform method: LOG
2025-08-26 05:59:26.311952 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:26.322998 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:26.334606 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:26.556089 INFO::Creating fits folder
2025-08-26 05:59:26.559126 INFO::Writing residuals to file /tmp/Rtmp3XwaYS/filebe021a03c846/fits/residuals_linear.rds
2025-08-26 05:59:26.562983 INFO::Writing fitted values to file /tmp/Rtmp3XwaYS/filebe021a03c846/fits/fitted_linear.rds
2025-08-26 05:59:26.567893 INFO::Writing residuals to file /tmp/Rtmp3XwaYS/filebe021a03c846/fits/residuals_logistic.rds
2025-08-26 05:59:26.571739 INFO::Writing fitted values to file /tmp/Rtmp3XwaYS/filebe021a03c846/fits/fitted_logistic.rds
2025-08-26 05:59:26.57924 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmp3XwaYS/filebe021a03c846/all_results.tsv
2025-08-26 05:59:26.584447 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): /tmp/Rtmp3XwaYS/filebe021a03c846/significant_results.tsv
2025-08-26 05:59:26.588921 INFO::Creating output figures folder
2025-08-26 05:59:26.593381 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmp3XwaYS/filebe021a03c846/figures/summary_plot.pdf
2025-08-26 05:59:29.43916 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp3XwaYS/filebe021a03c846/figures
2025-08-26 05:59:29.443027 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-26 05:59:29.454753 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-26 05:59:30.263351 INFO::Writing summary plot of
                        significant results to file: /tmp/Rtmp3XwaYS/filebe021a03c846/figures/summary_plot.pdf
2025-08-26 05:59:33.142186 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp3XwaYS/filebe021a03c846/figures
2025-08-26 05:59:33.14569 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-26 05:59:33.158213 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-26 05:59:34.039326 INFO::Running the linear model component
2025-08-26 05:59:34.068146 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:34.078447 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:34.089169 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:34.111906 INFO::Counting total values for each feature
2025-08-26 05:59:34.116073 INFO::Running the logistic model component
2025-08-26 05:59:34.140635 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:34.157284 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:34.173053 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:34.197382 INFO::Counting total values for each feature
2025-08-26 05:59:34.202404 INFO::Re-running abundances for warn_prevalence
2025-08-26 05:59:34.204528 INFO::Running selected normalization method: TSS
2025-08-26 05:59:34.207981 INFO::Running selected transform method: LOG
2025-08-26 05:59:34.231865 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:34.242498 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:34.253045 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:34.493513 INFO::Creating output folder
2025-08-26 05:59:34.495949 INFO::Creating output figures folder
2025-08-26 05:59:34.500352 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmp3XwaYS/filebe021575f614/figures/summary_plot.pdf
2025-08-26 05:59:37.516323 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmp3XwaYS/filebe021575f614/figures
2025-08-26 05:59:37.519836 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-26 05:59:37.532294 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-26 05:59:39.695065 INFO::Applying z-score to standardize continuous metadata
2025-08-26 05:59:39.713066 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-26 05:59:39.715354 INFO::Bypass z-score application to metadata
2025-08-26 05:59:39.721072 INFO::Bypass z-score application to metadata
2025-08-26 05:59:39.770165 INFO::Determining format of input files
2025-08-26 05:59:39.772894 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-26 05:59:39.777226 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-26 05:59:39.796285 INFO::Determining format of input files
2025-08-26 05:59:39.799627 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-26 05:59:39.803055 INFO::Input format is feature_specific_covariate samples as columns
2025-08-26 05:59:39.824462 INFO::Determining format of input files
2025-08-26 05:59:39.826845 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-26 05:59:39.829187 INFO::Input format is feature_specific_covariate samples as columns
2025-08-26 05:59:39.83331 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-26 05:59:39.835521 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-26 05:59:39.863577 INFO::Running selected transform method: LOG
2025-08-26 05:59:39.866269 INFO::Creating output feature tables folder
2025-08-26 05:59:39.868746 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3XwaYS/filebe026ad64b23/features/data_transformed.tsv
2025-08-26 05:59:39.879127 INFO::Running selected transform method: LOG
2025-08-26 05:59:39.883632 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3XwaYS/filebe026ad64b23/features/data_transformed.tsv
2025-08-26 05:59:39.894265 INFO::Running selected transform method: PLOG
2025-08-26 05:59:39.898166 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3XwaYS/filebe026ad64b23/features/data_transformed.tsv
2025-08-26 05:59:39.905254 INFO::Running selected transform method: NONE
2025-08-26 05:59:39.907359 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmp3XwaYS/filebe026ad64b23/features/data_transformed.tsv
2025-08-26 05:59:39.929585 INFO::Running the linear model component
2025-08-26 05:59:39.952918 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:39.963395 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:39.973731 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:39.991867 INFO::Counting total values for each feature
2025-08-26 05:59:39.996025 INFO::Running the logistic model component
2025-08-26 05:59:40.019421 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:40.036962 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:40.052165 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:40.075253 INFO::Counting total values for each feature
2025-08-26 05:59:40.080346 INFO::Re-running abundances for warn_prevalence
2025-08-26 05:59:40.082341 INFO::Running selected normalization method: TSS
2025-08-26 05:59:40.085601 INFO::Running selected transform method: LOG
2025-08-26 05:59:40.110657 INFO::Fitting model to feature number 1, a
2025-08-26 05:59:40.12157 INFO::Fitting model to feature number 2, b
2025-08-26 05:59:40.133022 INFO::Fitting model to feature number 3, c
2025-08-26 05:59:40.361746 INFO::Creating output folder
2025-08-26 05:59:40.36407 INFO::Creating fits folder
2025-08-26 05:59:40.36655 INFO::Writing residuals to file /tmp/Rtmp3XwaYS/filebe021adf1da1/fits/residuals_linear.rds
2025-08-26 05:59:40.369215 INFO::Writing fitted values to file /tmp/Rtmp3XwaYS/filebe021adf1da1/fits/fitted_linear.rds
2025-08-26 05:59:40.371732 INFO::Writing residuals to file /tmp/Rtmp3XwaYS/filebe021adf1da1/fits/residuals_logistic.rds
2025-08-26 05:59:40.37427 INFO::Writing fitted values to file /tmp/Rtmp3XwaYS/filebe021adf1da1/fits/fitted_logistic.rds
2025-08-26 05:59:40.381659 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmp3XwaYS/filebe021adf1da1/all_results.tsv
2025-08-26 05:59:40.3872 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): /tmp/Rtmp3XwaYS/filebe021adf1da1/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
670.223  11.716 701.750 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin340.897 1.53845.354
maaslin_check_arguments0.2810.0070.296
maaslin_check_formula0.2920.0150.349
maaslin_compute_formula0.2980.0140.320
maaslin_contrast_test43.329 1.79848.218
maaslin_filter1.1600.0821.343
maaslin_fit31.424 1.00236.928
maaslin_log_arguments0.2860.0180.660
maaslin_normalize0.6860.0691.222
maaslin_plot_results82.518 1.79688.763
maaslin_plot_results_from_output81.522 1.34787.599
maaslin_process_metadata1.2200.0721.363
maaslin_read_data0.2770.0140.307
maaslin_reorder_data0.3020.0170.347
maaslin_transform1.5200.1171.707
maaslin_write_results32.921 0.96836.221
maaslin_write_results_lefse_format37.420 0.78940.762
preprocess_dna_mtx0.0090.0010.009
preprocess_taxa_mtx0.0090.0010.012