Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-06-19 12:05 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4493
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 1143/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 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 kjohnson3

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: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.1.0.tar.gz
StartedAt: 2025-06-18 19:54:58 -0400 (Wed, 18 Jun 2025)
EndedAt: 2025-06-18 19:59:27 -0400 (Wed, 18 Jun 2025)
EllapsedTime: 269.4 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results               13.890  0.779  14.790
maaslin_plot_results_from_output   13.393  0.806  14.280
maaslin3                            7.917  0.495   8.466
maaslin_contrast_test               7.386  0.635   8.069
maaslin_write_results_lefse_format  6.017  0.524   6.580
maaslin_write_results               5.338  0.618   5.958
maaslin_fit                         4.874  0.579   5.456
* 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-arm64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.1.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(maaslin3)
> 
> test_check("maaslin3")
2025-06-18 19:57:19.971772 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:57:19.997885 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:57:20.026164 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:57:20.034315 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:57:20.052441 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:57:20.079247 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:57:20.081312 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:57:20.085595 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:57:20.124109 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:57:20.126208 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:57:20.143531 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:57:20.157966 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:57:20.162394 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:57:20.176586 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:57:20.205945 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:57:26.951759 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:57:26.978165 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:57:27.003577 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:57:27.011122 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:57:27.049413 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:57:27.078598 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:57:27.080653 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:57:27.08485 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:57:27.118614 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:57:27.120708 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:57:27.137723 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:57:27.151693 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:57:27.156085 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:57:27.170076 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:57:27.194123 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:57:28.396 R[63114:126733449] XType: Using static font registry.
2025-06-18 19:57:34.548083 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:57:34.587712 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:57:34.615237 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:57:34.622787 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:57:34.634483 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:57:34.659821 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:57:34.661769 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:57:34.665852 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:57:34.698569 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:57:34.70064 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:57:34.740612 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:57:34.754315 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:57:34.758621 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:57:34.772408 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:57:34.79615 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:57:40.769584 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:57:40.796714 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:57:40.822932 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:57:40.830295 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:57:40.841553 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:57:40.868935 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:57:40.871051 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:57:40.875544 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:57:40.913165 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:57:40.915384 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:57:40.934472 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:57:40.950186 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:57:40.955244 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:57:40.971159 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:57:40.996757 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:57:41.084471 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/residuals_linear.rds
2025-06-18 19:57:41.117326 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/fitted_linear.rds
2025-06-18 19:57:41.150678 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/residuals_logistic.rds
2025-06-18 19:57:41.316635 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/fitted_logistic.rds
2025-06-18 19:57:47.697274 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:57:47.723063 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:57:47.74861 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:57:47.756291 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:57:47.767954 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:57:47.794676 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:57:47.796705 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:57:47.800884 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:57:47.833948 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:57:47.836068 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:57:47.853325 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:57:47.867462 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:57:47.871765 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:57:47.886349 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:57:47.911831 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:57:53.076467 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:57:53.102988 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:57:53.129355 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:57:53.136941 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:57:53.148794 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:57:53.175824 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:57:53.17822 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:57:53.182669 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:57:53.21486 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:57:53.216844 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:57:53.237085 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:57:53.252546 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:57:53.25732 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:57:53.272823 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:57:53.300326 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:57:53.377185 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/residuals_linear.rds
2025-06-18 19:57:53.409546 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/fitted_linear.rds
2025-06-18 19:57:53.444204 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/residuals_logistic.rds
2025-06-18 19:57:53.614561 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/fitted_logistic.rds
2025-06-18 19:58:00.137649 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:58:00.162929 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:58:00.188407 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:58:00.196303 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:58:00.208392 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:58:00.234356 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:58:00.236348 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:58:00.240435 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:58:00.273203 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:58:00.275214 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:58:00.292181 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:58:00.305826 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:58:00.310017 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:58:00.34345 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:58:00.36595 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:58:05.307645 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:58:05.334372 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:58:05.360143 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:58:05.367884 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:58:05.380167 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:58:05.407327 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:58:05.409518 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:58:05.413768 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:58:05.447792 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:58:05.449982 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:58:05.467176 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:58:05.48188 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:58:05.48606 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:58:05.499892 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:58:05.52326 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:58:05.599336 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/residuals_linear.rds
2025-06-18 19:58:05.632389 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/fitted_linear.rds
2025-06-18 19:58:05.666464 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/residuals_logistic.rds
2025-06-18 19:58:05.843393 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a28bcde49/fits/fitted_logistic.rds
2025-06-18 19:58:12.45659 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:58:12.483766 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:58:12.512952 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:58:12.521685 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:58:12.533848 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:58:12.565705 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:58:12.567843 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:58:12.572185 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:58:12.609302 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:58:12.611527 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:58:12.629296 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:58:12.643283 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:58:12.647584 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:58:12.661845 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:58:12.68623 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:58:17.952622 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:58:17.979998 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:58:18.014824 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:58:18.023193 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:58:18.035929 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:58:18.063716 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:58:18.067739 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:58:18.072342 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:58:18.106732 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:58:18.108788 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:58:18.12529 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:58:18.138904 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:58:18.143065 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:58:18.156381 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:58:18.180405 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:58:25.677354 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:58:29.569435 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:58:37.917245 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:58:41.749357 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:58:41.937067 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_linear.rds
2025-06-18 19:58:41.972534 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_linear.rds
2025-06-18 19:58:41.995107 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_logistic.rds
2025-06-18 19:58:42.035511 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_logistic.rds
2025-06-18 19:58:49.317495 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:58:51.911151 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:58:52.006443 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_linear.rds
2025-06-18 19:58:52.039484 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_linear.rds
2025-06-18 19:58:52.061822 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_logistic.rds
2025-06-18 19:58:52.101916 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_logistic.rds
2025-06-18 19:58:57.978268 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:59:00.190762 WARNING::Fitting problem for feature 124 returning NA
2025-06-18 19:59:00.291063 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_linear.rds
2025-06-18 19:59:00.323978 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_linear.rds
2025-06-18 19:59:00.346628 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_logistic.rds
2025-06-18 19:59:00.386529 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_logistic.rds
2025-06-18 19:59:06.799446 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:59:06.825935 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:59:06.852 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:59:06.859736 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:59:06.871687 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:59:06.911785 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:59:06.914038 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:59:06.918417 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:59:06.950101 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:59:06.952034 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:59:06.967972 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:59:06.981047 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:59:06.985112 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:59:06.997907 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:59:07.019799 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:59:11.574735 WARNING::Fitting problem for feature 50 returning NA
2025-06-18 19:59:11.601969 WARNING::Fitting problem for feature 62 returning NA
2025-06-18 19:59:11.629359 WARNING::Fitting problem for feature 74 returning NA
2025-06-18 19:59:11.637027 WARNING::Fitting problem for feature 78 returning NA
2025-06-18 19:59:11.648829 WARNING::Fitting problem for feature 84 returning NA
2025-06-18 19:59:11.674155 WARNING::Fitting problem for feature 96 returning NA
2025-06-18 19:59:11.676123 WARNING::Fitting problem for feature 97 returning NA
2025-06-18 19:59:11.680033 WARNING::Fitting problem for feature 99 returning NA
2025-06-18 19:59:11.712086 WARNING::Fitting problem for feature 114 returning NA
2025-06-18 19:59:11.714049 WARNING::Fitting problem for feature 115 returning NA
2025-06-18 19:59:11.730544 WARNING::Fitting problem for feature 123 returning NA
2025-06-18 19:59:11.743974 WARNING::Fitting problem for feature 130 returning NA
2025-06-18 19:59:11.748181 WARNING::Fitting problem for feature 132 returning NA
2025-06-18 19:59:11.762132 WARNING::Fitting problem for feature 139 returning NA
2025-06-18 19:59:11.786121 WARNING::Fitting problem for feature 150 returning NA
2025-06-18 19:59:12.340272 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_linear.rds
2025-06-18 19:59:12.372794 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_linear.rds
2025-06-18 19:59:12.40582 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/residuals_logistic.rds
2025-06-18 19:59:12.575477 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a31ffaada/fits/fitted_logistic.rds
2025-06-18 19:59:18.860124 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-06-18 19:59:18.86569 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-06-18 19:59:18.869414 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-06-18 19:59:18.886262 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-06-18 19:59:18.89181 ERROR::Effect name not found in metadata: d
2025-06-18 19:59:18.895583 ERROR::No user formula provided
2025-06-18 19:59:18.905791 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-06-18 19:59:18.909871 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-06-18 19:59:19.924567 INFO::Writing function arguments to log file
2025-06-18 19:59:19.929495 INFO::Verifying options selected are valid
2025-06-18 19:59:20.625917 INFO::Writing function arguments to log file
2025-06-18 19:59:20.630701 INFO::Verifying options selected are valid
2025-06-18 19:59:20.631093 INFO::Determining format of input files
2025-06-18 19:59:20.631409 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-18 19:59:20.632205 INFO::Running selected normalization method: TSS
2025-06-18 19:59:20.632722 INFO::Creating output feature tables folder
2025-06-18 19:59:20.633136 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/features/data_norm.tsv
2025-06-18 19:59:20.633792 INFO::Filter data based on min abundance and min prevalence
2025-06-18 19:59:20.634216 INFO::Total samples in data: 16
2025-06-18 19:59:20.634549 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-06-18 19:59:20.635202 INFO::Total filtered features: 0
2025-06-18 19:59:20.635552 INFO::Filtered feature names from abundance and prevalence filtering:
2025-06-18 19:59:20.635938 INFO::Total features filtered by non-zero variance filtering: 0
2025-06-18 19:59:20.636267 INFO::Filtered feature names from variance filtering:
2025-06-18 19:59:20.636582 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/features/filtered_data.tsv
2025-06-18 19:59:20.637204 INFO::Running selected transform method: LOG
2025-06-18 19:59:20.637631 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/features/data_transformed.tsv
2025-06-18 19:59:20.638317 INFO::Applying z-score to standardize continuous metadata
2025-06-18 19:59:20.640214 INFO::Running the linear model component
2025-06-18 19:59:20.64731 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:20.648923 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:20.650806 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:20.653774 INFO::Counting total values for each feature
2025-06-18 19:59:20.654486 INFO::Running the logistic model component
2025-06-18 19:59:20.660266 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:20.662734 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:20.664746 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:20.667727 INFO::Counting total values for each feature
2025-06-18 19:59:20.668526 INFO::Re-running abundances for warn_prevalence
2025-06-18 19:59:20.668871 INFO::Running selected normalization method: TSS
2025-06-18 19:59:20.669397 INFO::Running selected transform method: LOG
2025-06-18 19:59:20.67501 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:20.676483 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:20.677871 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:20.705392 INFO::Creating fits folder
2025-06-18 19:59:20.705992 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/fits/residuals_linear.rds
2025-06-18 19:59:20.706646 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/fits/fitted_linear.rds
2025-06-18 19:59:20.707179 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/fits/residuals_logistic.rds
2025-06-18 19:59:20.707708 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/fits/fitted_logistic.rds
2025-06-18 19:59:20.708689 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/all_results.tsv
2025-06-18 19:59:20.709443 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/significant_results.tsv
2025-06-18 19:59:20.710048 INFO::Creating output figures folder
2025-06-18 19:59:20.710576 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/figures/summary_plot.pdf
2025-06-18 19:59:21.186987 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/figures
2025-06-18 19:59:21.187813 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-18 19:59:21.189737 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-18 19:59:21.340234 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/figures/summary_plot.pdf
2025-06-18 19:59:21.804961 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a112c81ad/figures
2025-06-18 19:59:21.805567 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-18 19:59:21.80747 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-18 19:59:21.959106 INFO::Running the linear model component
2025-06-18 19:59:21.962098 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:21.96365 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:21.964896 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:21.967415 INFO::Counting total values for each feature
2025-06-18 19:59:21.967984 INFO::Running the logistic model component
2025-06-18 19:59:21.970605 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:21.972693 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:21.974508 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:21.977318 INFO::Counting total values for each feature
2025-06-18 19:59:21.977986 INFO::Re-running abundances for warn_prevalence
2025-06-18 19:59:21.978224 INFO::Running selected normalization method: TSS
2025-06-18 19:59:21.978653 INFO::Running selected transform method: LOG
2025-06-18 19:59:21.981316 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:21.982637 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:21.983796 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:22.011578 INFO::Creating output folder
2025-06-18 19:59:22.012079 INFO::Creating output figures folder
2025-06-18 19:59:22.012531 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a157f2db9/figures/summary_plot.pdf
2025-06-18 19:59:22.516237 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a157f2db9/figures
2025-06-18 19:59:22.516872 INFO::Plotting associations from most to least significant, grouped by metadata
2025-06-18 19:59:22.518734 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-06-18 19:59:22.865133 INFO::Applying z-score to standardize continuous metadata
2025-06-18 19:59:22.868278 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-06-18 19:59:22.868574 INFO::Bypass z-score application to metadata
2025-06-18 19:59:22.869313 INFO::Bypass z-score application to metadata
2025-06-18 19:59:22.875619 INFO::Determining format of input files
2025-06-18 19:59:22.875916 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-18 19:59:22.876158 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-06-18 19:59:22.878194 INFO::Determining format of input files
2025-06-18 19:59:22.878498 INFO::Input format is data samples as columns and metadata samples as rows
2025-06-18 19:59:22.878869 INFO::Input format is feature_specific_covariate samples as columns
2025-06-18 19:59:22.881115 INFO::Determining format of input files
2025-06-18 19:59:22.881384 INFO::Input format is data samples as rows and metadata samples as rows
2025-06-18 19:59:22.881679 INFO::Input format is feature_specific_covariate samples as columns
2025-06-18 19:59:22.882119 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-06-18 19:59:22.88233 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-06-18 19:59:22.885642 INFO::Running selected transform method: LOG
2025-06-18 19:59:22.885972 INFO::Creating output feature tables folder
2025-06-18 19:59:22.88633 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a4b0348f6/features/data_transformed.tsv
2025-06-18 19:59:22.887572 INFO::Running selected transform method: LOG
2025-06-18 19:59:22.887876 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a4b0348f6/features/data_transformed.tsv
2025-06-18 19:59:22.888975 INFO::Running selected transform method: PLOG
2025-06-18 19:59:22.889446 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a4b0348f6/features/data_transformed.tsv
2025-06-18 19:59:22.890301 INFO::Running selected transform method: NONE
2025-06-18 19:59:22.890533 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a4b0348f6/features/data_transformed.tsv
2025-06-18 19:59:22.892954 INFO::Running the linear model component
2025-06-18 19:59:22.895537 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:22.896901 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:22.898082 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:22.900327 INFO::Counting total values for each feature
2025-06-18 19:59:22.900861 INFO::Running the logistic model component
2025-06-18 19:59:22.903399 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:22.905329 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:22.907063 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:22.909706 INFO::Counting total values for each feature
2025-06-18 19:59:22.910347 INFO::Re-running abundances for warn_prevalence
2025-06-18 19:59:22.910572 INFO::Running selected normalization method: TSS
2025-06-18 19:59:22.910986 INFO::Running selected transform method: LOG
2025-06-18 19:59:22.913574 INFO::Fitting model to feature number 1, a
2025-06-18 19:59:22.914844 INFO::Fitting model to feature number 2, b
2025-06-18 19:59:22.915994 INFO::Fitting model to feature number 3, c
2025-06-18 19:59:22.943319 INFO::Creating output folder
2025-06-18 19:59:22.943786 INFO::Creating fits folder
2025-06-18 19:59:22.944088 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a44ab34f3/fits/residuals_linear.rds
2025-06-18 19:59:22.944537 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a44ab34f3/fits/fitted_linear.rds
2025-06-18 19:59:22.946725 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a44ab34f3/fits/residuals_logistic.rds
2025-06-18 19:59:22.948121 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a44ab34f3/fits/fitted_logistic.rds
2025-06-18 19:59:22.949785 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a44ab34f3/all_results.tsv
2025-06-18 19:59:22.950396 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpXMyXEI/filef68a44ab34f3/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
120.943   5.481 127.688

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin37.9170.4958.466
maaslin_check_arguments0.0720.0030.081
maaslin_check_formula0.0570.0020.061
maaslin_compute_formula0.0520.0030.056
maaslin_contrast_test7.3860.6358.069
maaslin_filter0.2050.0160.221
maaslin_fit4.8740.5795.456
maaslin_log_arguments0.0530.0030.057
maaslin_normalize0.1330.0120.146
maaslin_plot_results13.890 0.77914.790
maaslin_plot_results_from_output13.393 0.80614.280
maaslin_process_metadata0.2170.0210.238
maaslin_read_data0.0580.0030.061
maaslin_reorder_data0.0580.0050.061
maaslin_transform0.2700.0240.294
maaslin_write_results5.3380.6185.958
maaslin_write_results_lefse_format6.0170.5246.580
preprocess_dna_mtx0.0020.0000.001
preprocess_taxa_mtx0.0010.0010.002