Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-04-17 11:44 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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: 2025-04-16 13:40 -0400 (Wed, 16 Apr 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 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 1.0.0
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: 2025-04-16 22:09:46 -0400 (Wed, 16 Apr 2025)
EndedAt: 2025-04-16 22:22:32 -0400 (Wed, 16 Apr 2025)
EllapsedTime: 766.8 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 4.5.0 RC (2025-04-04 r88126)
* 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_from_output   41.491  1.030  42.874
maaslin_plot_results               40.897  1.338  42.508
maaslin3                           23.048  1.168  24.590
maaslin_contrast_test              21.713  1.189  23.358
maaslin_write_results_lefse_format 17.376  0.766  18.223
maaslin_write_results              15.915  0.588  16.628
maaslin_fit                        14.193  0.544  14.824
* 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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")
2025-04-16 22:16:36.25545 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:16:36.355173 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:16:36.486579 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:16:36.516297 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:16:36.558506 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:16:36.668986 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:16:36.677439 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:16:36.693143 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:16:36.833987 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:16:36.841169 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:16:36.907709 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:16:36.954098 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:16:36.97003 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:16:37.037276 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:16:37.129951 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:16:55.394739 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:16:55.492785 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:16:55.588682 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:16:55.613302 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:16:55.677269 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:16:55.775055 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:16:55.782477 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:16:55.797245 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:16:55.915323 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:16:55.923324 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:16:55.988339 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:16:56.036835 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:16:56.052066 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:16:56.106658 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:16:56.184735 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:16:59.746 R[53796:688799235] XType: com.apple.fonts is not accessible.
2025-04-16 22:16:59.746 R[53796:688799235] XType: XTFontStaticRegistry is enabled.
2025-04-16 22:17:17.224218 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:17:17.323486 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:17:17.433782 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:17:17.467507 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:17:17.51147 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:17:17.614476 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:17:17.620962 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:17:17.634847 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:17:17.748723 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:17:17.755695 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:17:17.826452 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:17:17.88093 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:17:17.897351 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:17:17.956592 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:17:18.051471 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:17:32.864401 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:17:32.967334 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:17:33.073676 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:17:33.099477 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:17:33.182673 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:17:33.286366 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:17:33.294878 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:17:33.315155 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:17:33.44609 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:17:33.453033 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:17:33.52447 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:17:33.580547 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:17:33.596368 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:17:33.651594 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:17:33.739055 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:17:34.003705 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/residuals_linear.rds
2025-04-16 22:17:34.072414 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/fitted_linear.rds
2025-04-16 22:17:34.144578 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/residuals_logistic.rds
2025-04-16 22:17:34.5071 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/fitted_logistic.rds
2025-04-16 22:17:53.541738 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:17:53.646197 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:17:53.748976 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:17:53.777613 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:17:53.825527 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:17:53.928964 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:17:53.937684 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:17:53.957704 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:17:54.092754 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:17:54.100575 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:17:54.165644 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:17:54.216307 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:17:54.233508 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:17:54.421593 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:17:54.513309 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:18:09.324469 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:18:09.417456 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:18:09.511714 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:18:09.545088 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:18:09.588887 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:18:09.684864 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:18:09.691425 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:18:09.706201 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:18:09.831946 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:18:09.841601 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:18:09.913124 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:18:09.969076 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:18:09.987435 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:18:10.043539 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:18:10.137211 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:18:10.402207 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/residuals_linear.rds
2025-04-16 22:18:10.476297 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/fitted_linear.rds
2025-04-16 22:18:10.551587 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/residuals_logistic.rds
2025-04-16 22:18:10.889277 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/fitted_logistic.rds
2025-04-16 22:18:29.360547 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:18:29.457934 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:18:29.55154 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:18:29.580018 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:18:29.624661 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:18:29.718543 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:18:29.724526 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:18:29.742739 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:18:29.862944 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:18:29.870562 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:18:29.934701 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:18:30.033123 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:18:30.048595 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:18:30.109244 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:18:30.19789 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:18:44.741163 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:18:44.876732 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:18:44.972792 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:18:45.003333 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:18:45.05041 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:18:45.149682 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:18:45.159163 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:18:45.178626 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:18:45.314136 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:18:45.322602 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:18:45.394545 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:18:45.446989 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:18:45.463156 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:18:45.521388 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:18:45.603399 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:18:45.859292 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/residuals_linear.rds
2025-04-16 22:18:45.93507 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/fitted_linear.rds
2025-04-16 22:18:46.006814 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/residuals_logistic.rds
2025-04-16 22:18:46.365797 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2244ce2e5a0/fits/fitted_logistic.rds
2025-04-16 22:19:04.745406 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:19:04.852854 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:19:04.951147 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:19:04.980406 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:19:05.022605 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:19:05.122575 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:19:05.130519 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:19:05.148566 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:19:05.27148 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:19:05.279873 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:19:05.337356 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:19:05.385281 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:19:05.398706 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:19:05.452238 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:19:05.544985 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:19:19.410398 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:19:19.548599 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:19:19.638637 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:19:19.664593 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:19:19.705246 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:19:19.808137 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:19:19.815114 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:19:19.833413 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:19:19.954657 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:19:19.9636 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:19:20.028031 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:19:20.077322 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:19:20.093999 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:19:20.145931 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:19:20.231936 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:19:41.664945 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:19:52.611212 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:20:14.957054 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:20:25.663176 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:20:26.449896 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_linear.rds
2025-04-16 22:20:26.520073 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_linear.rds
2025-04-16 22:20:26.566223 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_logistic.rds
2025-04-16 22:20:26.645589 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_logistic.rds
2025-04-16 22:20:46.745459 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:20:53.789955 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:20:54.203034 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_linear.rds
2025-04-16 22:20:54.272684 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_linear.rds
2025-04-16 22:20:54.311926 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_logistic.rds
2025-04-16 22:20:54.384246 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_logistic.rds
2025-04-16 22:21:10.646647 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:21:17.8485 WARNING::Fitting problem for feature 124 returning NA
2025-04-16 22:21:18.231262 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_linear.rds
2025-04-16 22:21:18.300125 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_linear.rds
2025-04-16 22:21:18.341272 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_logistic.rds
2025-04-16 22:21:18.410255 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_logistic.rds
2025-04-16 22:21:34.106255 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:21:34.195204 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:21:34.289646 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:21:34.317244 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:21:34.359177 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:21:34.444145 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:21:34.45287 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:21:34.470428 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:21:34.595147 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:21:34.603637 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:21:34.664198 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:21:34.716608 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:21:34.729532 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:21:34.78436 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:21:34.868262 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:21:48.799187 WARNING::Fitting problem for feature 50 returning NA
2025-04-16 22:21:48.896497 WARNING::Fitting problem for feature 62 returning NA
2025-04-16 22:21:48.994767 WARNING::Fitting problem for feature 74 returning NA
2025-04-16 22:21:49.023646 WARNING::Fitting problem for feature 78 returning NA
2025-04-16 22:21:49.070086 WARNING::Fitting problem for feature 84 returning NA
2025-04-16 22:21:49.172292 WARNING::Fitting problem for feature 96 returning NA
2025-04-16 22:21:49.179342 WARNING::Fitting problem for feature 97 returning NA
2025-04-16 22:21:49.193609 WARNING::Fitting problem for feature 99 returning NA
2025-04-16 22:21:49.32698 WARNING::Fitting problem for feature 114 returning NA
2025-04-16 22:21:49.335716 WARNING::Fitting problem for feature 115 returning NA
2025-04-16 22:21:49.409238 WARNING::Fitting problem for feature 123 returning NA
2025-04-16 22:21:49.4673 WARNING::Fitting problem for feature 130 returning NA
2025-04-16 22:21:49.484093 WARNING::Fitting problem for feature 132 returning NA
2025-04-16 22:21:49.540155 WARNING::Fitting problem for feature 139 returning NA
2025-04-16 22:21:49.634252 WARNING::Fitting problem for feature 150 returning NA
2025-04-16 22:21:49.950267 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_linear.rds
2025-04-16 22:21:50.026245 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_linear.rds
2025-04-16 22:21:50.094951 WARNING::Deleting existing residuals file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/residuals_logistic.rds
2025-04-16 22:21:50.453946 WARNING::Deleting existing fitted file: /tmp/RtmpLW2e0P/filed2247a8e786d/fits/fitted_logistic.rds
2025-04-16 22:22:08.073208 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-04-16 22:22:08.095128 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-04-16 22:22:08.109927 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-04-16 22:22:08.186344 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-04-16 22:22:08.208614 ERROR::Effect name not found in metadata: d
2025-04-16 22:22:08.223438 ERROR::No user formula provided
2025-04-16 22:22:08.255089 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-04-16 22:22:08.269017 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-04-16 22:22:11.690844 INFO::Writing function arguments to log file
2025-04-16 22:22:11.710071 INFO::Verifying options selected are valid
2025-04-16 22:22:13.784735 INFO::Writing function arguments to log file
2025-04-16 22:22:13.803771 INFO::Verifying options selected are valid
2025-04-16 22:22:13.805641 INFO::Determining format of input files
2025-04-16 22:22:13.807233 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-16 22:22:13.810184 INFO::Running selected normalization method: TSS
2025-04-16 22:22:13.811669 INFO::Creating output feature tables folder
2025-04-16 22:22:13.812954 INFO::Writing normalized data to file /tmp/RtmpLW2e0P/filed2247c1d1829/features/data_norm.tsv
2025-04-16 22:22:13.815697 INFO::Filter data based on min abundance and min prevalence
2025-04-16 22:22:13.817094 INFO::Total samples in data: 16
2025-04-16 22:22:13.818096 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-04-16 22:22:13.819932 INFO::Total filtered features: 0
2025-04-16 22:22:13.820942 INFO::Filtered feature names from abundance and prevalence filtering:
2025-04-16 22:22:13.822133 INFO::Total features filtered by non-zero variance filtering: 0
2025-04-16 22:22:13.823107 INFO::Filtered feature names from variance filtering:
2025-04-16 22:22:13.824034 INFO::Writing filtered data to file /tmp/RtmpLW2e0P/filed2247c1d1829/features/filtered_data.tsv
2025-04-16 22:22:13.82579 INFO::Running selected transform method: LOG
2025-04-16 22:22:13.827029 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLW2e0P/filed2247c1d1829/features/data_transformed.tsv
2025-04-16 22:22:13.828937 INFO::Applying z-score to standardize continuous metadata
2025-04-16 22:22:13.834033 INFO::Running the linear model component
2025-04-16 22:22:13.856628 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:13.861953 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:13.867779 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:13.878626 INFO::Counting total values for each feature
2025-04-16 22:22:13.881452 INFO::Running the logistic model component
2025-04-16 22:22:13.902885 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:13.912152 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:13.920408 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:13.932723 INFO::Counting total values for each feature
2025-04-16 22:22:13.935534 INFO::Re-running abundances for warn_prevalence
2025-04-16 22:22:13.936989 INFO::Running selected normalization method: TSS
2025-04-16 22:22:13.939219 INFO::Running selected transform method: LOG
2025-04-16 22:22:13.960842 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:13.966046 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:13.971591 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:14.094788 INFO::Creating fits folder
2025-04-16 22:22:14.097145 INFO::Writing residuals to file /tmp/RtmpLW2e0P/filed2247c1d1829/fits/residuals_linear.rds
2025-04-16 22:22:14.09882 INFO::Writing fitted values to file /tmp/RtmpLW2e0P/filed2247c1d1829/fits/fitted_linear.rds
2025-04-16 22:22:14.100937 INFO::Writing residuals to file /tmp/RtmpLW2e0P/filed2247c1d1829/fits/residuals_logistic.rds
2025-04-16 22:22:14.102859 INFO::Writing fitted values to file /tmp/RtmpLW2e0P/filed2247c1d1829/fits/fitted_logistic.rds
2025-04-16 22:22:14.107104 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpLW2e0P/filed2247c1d1829/all_results.tsv
2025-04-16 22:22:14.110179 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/RtmpLW2e0P/filed2247c1d1829/significant_results.tsv
2025-04-16 22:22:14.112983 INFO::Creating output figures folder
2025-04-16 22:22:14.115389 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpLW2e0P/filed2247c1d1829/figures/summary_plot.pdf
2025-04-16 22:22:15.625531 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpLW2e0P/filed2247c1d1829/figures
2025-04-16 22:22:15.628457 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-16 22:22:15.635612 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-16 22:22:16.09822 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpLW2e0P/filed2247c1d1829/figures/summary_plot.pdf
2025-04-16 22:22:17.630876 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpLW2e0P/filed2247c1d1829/figures
2025-04-16 22:22:17.632939 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-16 22:22:17.639543 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-16 22:22:18.083463 INFO::Running the linear model component
2025-04-16 22:22:18.096353 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:18.102868 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:18.1082 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:18.117113 INFO::Counting total values for each feature
2025-04-16 22:22:18.119714 INFO::Running the logistic model component
2025-04-16 22:22:18.131334 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:18.137853 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:18.145888 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:18.157365 INFO::Counting total values for each feature
2025-04-16 22:22:18.160316 INFO::Re-running abundances for warn_prevalence
2025-04-16 22:22:18.161152 INFO::Running selected normalization method: TSS
2025-04-16 22:22:18.16244 INFO::Running selected transform method: LOG
2025-04-16 22:22:18.173183 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:18.178461 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:18.183631 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:18.286734 INFO::Creating output folder
2025-04-16 22:22:18.287876 INFO::Creating output figures folder
2025-04-16 22:22:18.289158 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpLW2e0P/filed22443fbf212/figures/summary_plot.pdf
2025-04-16 22:22:19.788854 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpLW2e0P/filed22443fbf212/figures
2025-04-16 22:22:19.790289 INFO::Plotting associations from most to least significant, grouped by metadata
2025-04-16 22:22:19.796987 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-04-16 22:22:20.786087 INFO::Applying z-score to standardize continuous metadata
2025-04-16 22:22:20.797148 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-04-16 22:22:20.798188 INFO::Bypass z-score application to metadata
2025-04-16 22:22:20.801359 INFO::Bypass z-score application to metadata
2025-04-16 22:22:20.826709 INFO::Determining format of input files
2025-04-16 22:22:20.827972 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-16 22:22:20.829509 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-04-16 22:22:20.840422 INFO::Determining format of input files
2025-04-16 22:22:20.841575 INFO::Input format is data samples as columns and metadata samples as rows
2025-04-16 22:22:20.843112 INFO::Input format is feature_specific_covariate samples as columns
2025-04-16 22:22:20.852696 INFO::Determining format of input files
2025-04-16 22:22:20.85412 INFO::Input format is data samples as rows and metadata samples as rows
2025-04-16 22:22:20.855762 INFO::Input format is feature_specific_covariate samples as columns
2025-04-16 22:22:20.858185 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-04-16 22:22:20.859295 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-04-16 22:22:20.871838 INFO::Running selected transform method: LOG
2025-04-16 22:22:20.873151 INFO::Creating output feature tables folder
2025-04-16 22:22:20.87452 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLW2e0P/filed2246570ccd1/features/data_transformed.tsv
2025-04-16 22:22:20.880429 INFO::Running selected transform method: LOG
2025-04-16 22:22:20.881499 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLW2e0P/filed2246570ccd1/features/data_transformed.tsv
2025-04-16 22:22:20.886731 INFO::Running selected transform method: PLOG
2025-04-16 22:22:20.888958 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLW2e0P/filed2246570ccd1/features/data_transformed.tsv
2025-04-16 22:22:20.892742 INFO::Running selected transform method: NONE
2025-04-16 22:22:20.893607 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpLW2e0P/filed2246570ccd1/features/data_transformed.tsv
2025-04-16 22:22:20.902627 INFO::Running the linear model component
2025-04-16 22:22:20.912839 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:20.91935 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:20.923369 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:20.92995 INFO::Counting total values for each feature
2025-04-16 22:22:20.931903 INFO::Running the logistic model component
2025-04-16 22:22:20.944581 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:20.953396 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:20.960777 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:20.97062 INFO::Counting total values for each feature
2025-04-16 22:22:20.973855 INFO::Re-running abundances for warn_prevalence
2025-04-16 22:22:20.975214 INFO::Running selected normalization method: TSS
2025-04-16 22:22:20.977459 INFO::Running selected transform method: LOG
2025-04-16 22:22:20.985902 INFO::Fitting model to feature number 1, a
2025-04-16 22:22:20.991703 INFO::Fitting model to feature number 2, b
2025-04-16 22:22:20.995377 INFO::Fitting model to feature number 3, c
2025-04-16 22:22:21.095937 INFO::Creating output folder
2025-04-16 22:22:21.096981 INFO::Creating fits folder
2025-04-16 22:22:21.098216 INFO::Writing residuals to file /tmp/RtmpLW2e0P/filed2245096e15e/fits/residuals_linear.rds
2025-04-16 22:22:21.099281 INFO::Writing fitted values to file /tmp/RtmpLW2e0P/filed2245096e15e/fits/fitted_linear.rds
2025-04-16 22:22:21.100298 INFO::Writing residuals to file /tmp/RtmpLW2e0P/filed2245096e15e/fits/residuals_logistic.rds
2025-04-16 22:22:21.101321 INFO::Writing fitted values to file /tmp/RtmpLW2e0P/filed2245096e15e/fits/fitted_logistic.rds
2025-04-16 22:22:21.104955 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpLW2e0P/filed2245096e15e/all_results.tsv
2025-04-16 22:22:21.107445 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/RtmpLW2e0P/filed2245096e15e/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
348.831   7.659 358.544

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin323.048 1.16824.590
maaslin_check_arguments0.1920.0060.198
maaslin_check_formula0.1910.0140.213
maaslin_compute_formula0.1910.0140.212
maaslin_contrast_test21.713 1.18923.358
maaslin_filter0.6370.0580.704
maaslin_fit14.193 0.54414.824
maaslin_log_arguments0.1500.0080.159
maaslin_normalize0.3880.0280.421
maaslin_plot_results40.897 1.33842.508
maaslin_plot_results_from_output41.491 1.03042.874
maaslin_process_metadata0.6280.0440.677
maaslin_read_data0.1530.0080.162
maaslin_reorder_data0.1710.0110.183
maaslin_transform0.8040.0580.872
maaslin_write_results15.915 0.58816.628
maaslin_write_results_lefse_format17.376 0.76618.223
preprocess_dna_mtx0.0050.0010.004
preprocess_taxa_mtx0.0060.0010.006