Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1147/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.1.0  (landing page)
William Nickols
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 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
lconwaymacOS 12.7.1 Monterey / x86_64  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


CHECK results for maaslin3 on lconway

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: 2025-08-08 21:58:53 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 22:11:57 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 783.9 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 4.5.1 (2025-06-13)
* 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 ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   42.399  1.261  44.083
maaslin_plot_results               41.957  1.081  43.365
maaslin3                           23.967  1.088  25.338
maaslin_contrast_test              20.144  1.026  21.479
maaslin_write_results              16.758  0.797  17.740
maaslin_write_results_lefse_format 16.990  0.530  17.636
maaslin_fit                        14.958  0.858  15.991
* 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 ‘1.1.0’
** 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 4.5.1 (2025-06-13) -- "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")
2025-08-08 22:05:53.433081 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:05:53.526094 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:05:53.633827 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:05:53.656709 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:05:53.711229 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:05:53.818249 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:05:53.825659 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:05:53.840436 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:05:53.980845 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:05:53.988813 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:05:54.046975 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:05:54.100771 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:05:54.114426 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:05:54.168558 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:05:54.272198 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:06:12.178327 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:06:12.282607 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:06:12.38085 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:06:12.409467 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:06:12.451714 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:06:12.546857 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:06:12.570639 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:06:12.585329 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:06:12.708112 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:06:12.715018 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:06:12.773585 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:06:12.821695 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:06:12.836119 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:06:12.890238 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:06:12.988063 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:06:16.619 R[41882:417872624] XType: com.apple.fonts is not accessible.
2025-08-08 22:06:16.620 R[41882:417872624] XType: XTFontStaticRegistry is enabled.
2025-08-08 22:06:33.481587 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:06:33.609075 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:06:33.713122 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:06:33.741098 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:06:33.791123 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:06:33.894061 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:06:33.901222 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:06:33.917301 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:06:34.049336 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:06:34.056716 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:06:34.182249 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:06:34.237414 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:06:34.253903 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:06:34.3135 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:06:34.406389 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:06:50.2349 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:06:50.326328 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:06:50.410807 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:06:50.433067 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:06:50.474465 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:06:50.560043 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:06:50.566486 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:06:50.581356 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:06:50.754742 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:06:50.762457 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:06:50.827061 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:06:50.884082 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:06:50.903423 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:06:50.959106 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:06:51.042517 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:06:51.290812 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_linear.rds
2025-08-08 22:06:51.363712 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_linear.rds
2025-08-08 22:06:51.429973 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_logistic.rds
2025-08-08 22:06:51.776411 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_logistic.rds
2025-08-08 22:07:11.541757 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:07:11.664379 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:07:11.760956 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:07:11.788222 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:07:11.832882 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:07:11.929877 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:07:11.937033 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:07:11.957088 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:07:12.089495 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:07:12.097359 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:07:12.180819 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:07:12.244359 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:07:12.260667 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:07:12.321856 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:07:12.432424 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:07:27.611478 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:07:27.715335 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:07:27.803085 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:07:27.826838 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:07:27.874588 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:07:27.961399 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:07:27.968202 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:07:27.985113 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:07:28.121299 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:07:28.128207 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:07:28.188705 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:07:28.24316 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:07:28.258695 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:07:28.317938 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:07:28.416695 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:07:28.69321 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_linear.rds
2025-08-08 22:07:28.760942 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_linear.rds
2025-08-08 22:07:28.833342 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_logistic.rds
2025-08-08 22:07:29.193722 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_logistic.rds
2025-08-08 22:07:48.279435 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:07:48.38293 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:07:48.494007 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:07:48.529661 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:07:48.588127 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:07:48.710232 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:07:48.719991 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:07:48.738795 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:07:48.893322 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:07:48.90158 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:07:48.971765 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:07:49.026222 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:07:49.040526 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:07:49.138859 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:07:49.22876 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:08:03.00125 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:08:03.103792 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:08:03.198738 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:08:03.224718 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:08:03.271592 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:08:03.36215 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:08:03.369242 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:08:03.385501 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:08:03.493096 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:08:03.49999 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:08:03.564443 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:08:03.614164 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:08:03.628393 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:08:03.678351 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:08:03.770669 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:08:04.011483 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_linear.rds
2025-08-08 22:08:04.078734 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_linear.rds
2025-08-08 22:08:04.149321 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/residuals_logistic.rds
2025-08-08 22:08:04.504071 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a2792ced9/fits/fitted_logistic.rds
2025-08-08 22:08:23.180601 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:08:23.27411 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:08:23.377335 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:08:23.409545 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:08:23.460815 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:08:23.563003 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:08:23.570468 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:08:23.587416 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:08:23.712439 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:08:23.719574 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:08:23.78424 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:08:23.838348 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:08:23.853854 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:08:23.949987 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:08:24.031817 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:08:38.120865 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:08:38.277355 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:08:38.363238 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:08:38.394998 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:08:38.44104 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:08:38.546181 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:08:38.555172 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:08:38.57403 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:08:38.72363 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:08:38.732796 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:08:38.801738 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:08:38.854124 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:08:38.87218 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:08:38.92442 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:08:39.019439 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:09:01.300377 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:09:13.296213 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:09:36.283152 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:09:47.321437 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:09:48.047578 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds
2025-08-08 22:09:48.121365 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds
2025-08-08 22:09:48.165598 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds
2025-08-08 22:09:48.243186 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds
2025-08-08 22:10:08.689741 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:10:14.76974 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:10:15.147543 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds
2025-08-08 22:10:15.222559 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds
2025-08-08 22:10:15.266221 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds
2025-08-08 22:10:15.341852 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds
2025-08-08 22:10:33.111742 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:10:39.39463 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 22:10:39.766618 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds
2025-08-08 22:10:39.833208 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds
2025-08-08 22:10:39.872701 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds
2025-08-08 22:10:39.949107 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds
2025-08-08 22:10:56.905286 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:10:56.993294 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:10:57.086713 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:10:57.114151 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:10:57.160282 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:10:57.253725 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:10:57.260202 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:10:57.274453 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:10:57.405228 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:10:57.414005 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:10:57.474922 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:10:57.532105 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:10:57.550513 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:10:57.60276 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:10:57.68745 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:11:11.292389 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 22:11:11.388987 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 22:11:11.485024 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 22:11:11.514261 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 22:11:11.559162 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 22:11:11.649423 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 22:11:11.655405 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 22:11:11.673567 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 22:11:11.796527 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 22:11:11.803154 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 22:11:11.875547 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 22:11:11.928698 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 22:11:11.944281 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 22:11:11.991454 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 22:11:12.082912 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 22:11:12.483289 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_linear.rds
2025-08-08 22:11:12.554627 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_linear.rds
2025-08-08 22:11:12.628802 WARNING::Deleting existing residuals file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/residuals_logistic.rds
2025-08-08 22:11:12.986611 WARNING::Deleting existing fitted file: /tmp/RtmpvHGJYs/filea39a74b47eaf/fits/fitted_logistic.rds
2025-08-08 22:11:31.026067 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-08 22:11:31.045544 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-08 22:11:31.061889 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-08 22:11:31.132434 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-08 22:11:31.153024 ERROR::Effect name not found in metadata: d
2025-08-08 22:11:31.165361 ERROR::No user formula provided
2025-08-08 22:11:31.199111 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-08 22:11:31.213678 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-08 22:11:34.827343 INFO::Writing function arguments to log file
2025-08-08 22:11:34.852511 INFO::Verifying options selected are valid
2025-08-08 22:11:36.929193 INFO::Writing function arguments to log file
2025-08-08 22:11:36.948331 INFO::Verifying options selected are valid
2025-08-08 22:11:36.95002 INFO::Determining format of input files
2025-08-08 22:11:36.951408 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 22:11:36.954087 INFO::Running selected normalization method: TSS
2025-08-08 22:11:36.955975 INFO::Creating output feature tables folder
2025-08-08 22:11:36.957377 INFO::Writing normalized data to file /tmp/RtmpvHGJYs/filea39a7e347ab/features/data_norm.tsv
2025-08-08 22:11:36.959829 INFO::Filter data based on min abundance and min prevalence
2025-08-08 22:11:36.961244 INFO::Total samples in data: 16
2025-08-08 22:11:36.96266 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-08 22:11:36.965325 INFO::Total filtered features: 0
2025-08-08 22:11:36.966772 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-08 22:11:36.96848 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-08 22:11:36.969486 INFO::Filtered feature names from variance filtering:
2025-08-08 22:11:36.970417 INFO::Writing filtered data to file /tmp/RtmpvHGJYs/filea39a7e347ab/features/filtered_data.tsv
2025-08-08 22:11:36.972866 INFO::Running selected transform method: LOG
2025-08-08 22:11:36.974599 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a7e347ab/features/data_transformed.tsv
2025-08-08 22:11:36.977178 INFO::Applying z-score to standardize continuous metadata
2025-08-08 22:11:36.983204 INFO::Running the linear model component
2025-08-08 22:11:37.004759 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:37.011434 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:37.017626 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:37.025365 INFO::Counting total values for each feature
2025-08-08 22:11:37.028327 INFO::Running the logistic model component
2025-08-08 22:11:37.047262 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:37.056815 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:37.06346 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:37.075399 INFO::Counting total values for each feature
2025-08-08 22:11:37.078773 INFO::Re-running abundances for warn_prevalence
2025-08-08 22:11:37.079943 INFO::Running selected normalization method: TSS
2025-08-08 22:11:37.08154 INFO::Running selected transform method: LOG
2025-08-08 22:11:37.103373 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:37.109529 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:37.114977 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:37.229179 INFO::Creating fits folder
2025-08-08 22:11:37.231317 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/residuals_linear.rds
2025-08-08 22:11:37.233802 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/fitted_linear.rds
2025-08-08 22:11:37.236483 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/residuals_logistic.rds
2025-08-08 22:11:37.238691 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a7e347ab/fits/fitted_logistic.rds
2025-08-08 22:11:37.242927 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpvHGJYs/filea39a7e347ab/all_results.tsv
2025-08-08 22:11:37.245408 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/RtmpvHGJYs/filea39a7e347ab/significant_results.tsv
2025-08-08 22:11:37.248132 INFO::Creating output figures folder
2025-08-08 22:11:37.249776 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpvHGJYs/filea39a7e347ab/figures/summary_plot.pdf
2025-08-08 22:11:38.654003 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvHGJYs/filea39a7e347ab/figures
2025-08-08 22:11:38.656287 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 22:11:38.661412 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 22:11:39.107873 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpvHGJYs/filea39a7e347ab/figures/summary_plot.pdf
2025-08-08 22:11:40.615314 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvHGJYs/filea39a7e347ab/figures
2025-08-08 22:11:40.617561 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 22:11:40.622128 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 22:11:41.083936 INFO::Running the linear model component
2025-08-08 22:11:41.097769 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:41.104402 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:41.109086 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:41.119594 INFO::Counting total values for each feature
2025-08-08 22:11:41.122343 INFO::Running the logistic model component
2025-08-08 22:11:41.132395 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:41.138547 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:41.144203 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:41.152546 INFO::Counting total values for each feature
2025-08-08 22:11:41.154698 INFO::Re-running abundances for warn_prevalence
2025-08-08 22:11:41.156015 INFO::Running selected normalization method: TSS
2025-08-08 22:11:41.158156 INFO::Running selected transform method: LOG
2025-08-08 22:11:41.172559 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:41.177388 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:41.18309 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:41.29612 INFO::Creating output folder
2025-08-08 22:11:41.297817 INFO::Creating output figures folder
2025-08-08 22:11:41.299968 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpvHGJYs/filea39a45016b4a/figures/summary_plot.pdf
2025-08-08 22:11:42.744556 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpvHGJYs/filea39a45016b4a/figures
2025-08-08 22:11:42.746853 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 22:11:42.753188 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 22:11:43.910851 INFO::Applying z-score to standardize continuous metadata
2025-08-08 22:11:43.921971 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-08 22:11:43.923429 INFO::Bypass z-score application to metadata
2025-08-08 22:11:43.927392 INFO::Bypass z-score application to metadata
2025-08-08 22:11:43.953092 INFO::Determining format of input files
2025-08-08 22:11:43.954468 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 22:11:43.955945 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-08 22:11:43.967094 INFO::Determining format of input files
2025-08-08 22:11:43.968663 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-08 22:11:43.970556 INFO::Input format is feature_specific_covariate samples as columns
2025-08-08 22:11:43.9816 INFO::Determining format of input files
2025-08-08 22:11:43.982644 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 22:11:43.9841 INFO::Input format is feature_specific_covariate samples as columns
2025-08-08 22:11:43.985893 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-08 22:11:43.986591 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-08 22:11:44.000399 INFO::Running selected transform method: LOG
2025-08-08 22:11:44.002231 INFO::Creating output feature tables folder
2025-08-08 22:11:44.003901 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv
2025-08-08 22:11:44.010055 INFO::Running selected transform method: LOG
2025-08-08 22:11:44.011229 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv
2025-08-08 22:11:44.015675 INFO::Running selected transform method: PLOG
2025-08-08 22:11:44.017153 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv
2025-08-08 22:11:44.02165 INFO::Running selected transform method: NONE
2025-08-08 22:11:44.022617 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpvHGJYs/filea39a1853bf68/features/data_transformed.tsv
2025-08-08 22:11:44.033955 INFO::Running the linear model component
2025-08-08 22:11:44.042351 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:44.046588 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:44.051269 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:44.060933 INFO::Counting total values for each feature
2025-08-08 22:11:44.063733 INFO::Running the logistic model component
2025-08-08 22:11:44.072385 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:44.080824 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:44.088059 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:44.098879 INFO::Counting total values for each feature
2025-08-08 22:11:44.102133 INFO::Re-running abundances for warn_prevalence
2025-08-08 22:11:44.103692 INFO::Running selected normalization method: TSS
2025-08-08 22:11:44.105618 INFO::Running selected transform method: LOG
2025-08-08 22:11:44.117872 INFO::Fitting model to feature number 1, a
2025-08-08 22:11:44.122918 INFO::Fitting model to feature number 2, b
2025-08-08 22:11:44.127754 INFO::Fitting model to feature number 3, c
2025-08-08 22:11:44.237956 INFO::Creating output folder
2025-08-08 22:11:44.239122 INFO::Creating fits folder
2025-08-08 22:11:44.240115 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/residuals_linear.rds
2025-08-08 22:11:44.241326 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/fitted_linear.rds
2025-08-08 22:11:44.242457 INFO::Writing residuals to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/residuals_logistic.rds
2025-08-08 22:11:44.243717 INFO::Writing fitted values to file /tmp/RtmpvHGJYs/filea39a223b5152/fits/fitted_logistic.rds
2025-08-08 22:11:44.247778 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpvHGJYs/filea39a223b5152/all_results.tsv
2025-08-08 22:11:44.250586 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/RtmpvHGJYs/filea39a223b5152/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
353.534   8.214 364.378 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin323.967 1.08825.338
maaslin_check_arguments0.1730.0040.180
maaslin_check_formula0.1710.0110.185
maaslin_compute_formula0.1880.0140.205
maaslin_contrast_test20.144 1.02621.479
maaslin_filter1.4130.2981.750
maaslin_fit14.958 0.85815.991
maaslin_log_arguments0.1720.0110.193
maaslin_normalize0.3520.0250.380
maaslin_plot_results41.957 1.08143.365
maaslin_plot_results_from_output42.399 1.26144.083
maaslin_process_metadata0.6580.0440.711
maaslin_read_data0.1700.0110.185
maaslin_reorder_data0.1820.0120.197
maaslin_transform0.8130.0740.906
maaslin_write_results16.758 0.79717.740
maaslin_write_results_lefse_format16.990 0.53017.636
preprocess_dna_mtx0.0030.0010.004
preprocess_taxa_mtx0.0040.0010.005