Back to Multiple platform build/check report for BioC 3.23:   simplified   long
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This page was generated on 2025-11-18 11:39 -0500 (Tue, 18 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4826
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4561
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4562
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 1152/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maaslin3 1.3.0  (landing page)
William Nickols
Snapshot Date: 2025-11-17 13:40 -0500 (Mon, 17 Nov 2025)
git_url: https://git.bioconductor.org/packages/maaslin3
git_branch: devel
git_last_commit: b274055
git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2025-11-18 03:17:30 -0500 (Tue, 18 Nov 2025)
EndedAt: 2025-11-18 03:28:31 -0500 (Tue, 18 Nov 2025)
EllapsedTime: 661.0 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* 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   35.038  1.290  36.660
maaslin_plot_results               33.527  0.927  34.668
maaslin_contrast_test              15.202  1.266  16.556
maaslin3                           14.898  0.908  15.835
maaslin_write_results_lefse_format 11.730  0.557  12.325
maaslin_write_results              10.674  0.787  11.497
maaslin_fit                        10.121  0.828  10.986
* 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/4.6-x86_64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.3.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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")
2025-11-18 03:23:44.715041 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:23:44.789096 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:23:44.879266 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:23:44.899052 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:23:44.93028 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:23:45.005049 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:23:45.010108 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:23:45.020344 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:23:45.106613 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:23:45.111484 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:23:45.155802 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:23:45.199681 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:23:45.209155 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:23:45.246225 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:23:45.306813 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:23:58.03589 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:23:58.101946 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:23:58.164538 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:23:58.182484 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:23:58.211465 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:23:58.297169 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:23:58.302052 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:23:58.312294 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:23:58.392402 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:23:58.397068 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:23:58.438355 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:23:58.472585 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:23:58.482645 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:23:58.515978 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:23:58.574377 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:24:01.854 R[13777:21467935] XType: Using static font registry.
2025-11-18 03:24:18.039584 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:24:18.103283 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:24:18.163194 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:24:18.181206 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:24:18.211041 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:24:18.282794 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:24:18.288205 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:24:18.299049 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:24:18.384824 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:24:18.390041 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:24:18.43665 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:24:18.474434 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:24:18.485187 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:24:18.522259 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:24:18.586075 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:24:29.246571 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:24:29.310984 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:24:29.397868 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:24:29.415895 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:24:29.444042 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:24:29.506226 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:24:29.510993 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:24:29.521277 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:24:29.599565 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:24:29.604299 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:24:29.644739 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:24:29.678345 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:24:29.688123 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:24:29.721636 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:24:29.778209 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:24:29.940891 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/residuals_linear.rds
2025-11-18 03:24:29.991146 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/fitted_linear.rds
2025-11-18 03:24:30.042294 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/residuals_logistic.rds
2025-11-18 03:24:30.293678 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/fitted_logistic.rds
2025-11-18 03:24:47.258152 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:24:47.319569 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:24:47.378995 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:24:47.397112 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:24:47.425422 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:24:47.491709 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:24:47.496661 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:24:47.507566 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:24:47.593364 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:24:47.598324 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:24:47.643976 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:24:47.680021 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:24:47.690951 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:24:47.723158 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:24:47.784874 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:24:57.61645 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:24:57.678088 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:24:57.736808 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:24:57.754166 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:24:57.781714 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:24:57.840655 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:24:57.845228 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:24:57.854909 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:24:57.930312 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:24:57.93525 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:24:57.973589 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:24:58.004353 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:24:58.014383 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:24:58.045657 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:24:58.098761 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:24:58.253723 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/residuals_linear.rds
2025-11-18 03:24:58.298522 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/fitted_linear.rds
2025-11-18 03:24:58.344378 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/residuals_logistic.rds
2025-11-18 03:24:58.58066 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/fitted_logistic.rds
2025-11-18 03:25:14.279289 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:25:14.340711 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:25:14.402257 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:25:14.420271 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:25:14.449154 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:25:14.550334 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:25:14.555111 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:25:14.565195 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:25:14.642585 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:25:14.64735 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:25:14.686775 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:25:14.718368 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:25:14.727774 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:25:14.759287 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:25:14.812599 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:25:24.803608 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:25:24.869973 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:25:24.933346 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:25:24.951886 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:25:24.98271 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:25:25.047009 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:25:25.051909 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:25:25.062222 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:25:25.143077 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:25:25.147845 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:25:25.190405 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:25:25.22483 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:25:25.235086 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:25:25.269727 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:25:25.329492 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:25:25.491635 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/residuals_linear.rds
2025-11-18 03:25:25.537514 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/fitted_linear.rds
2025-11-18 03:25:25.586229 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/residuals_logistic.rds
2025-11-18 03:25:25.838392 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d145511ea8/fits/fitted_logistic.rds
2025-11-18 03:25:42.592493 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:25:42.659992 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:25:42.724345 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:25:42.743984 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:25:42.774729 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:25:42.840272 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:25:42.845164 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:25:42.855591 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:25:42.9372 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:25:42.942293 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:25:42.985361 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:25:43.020012 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:25:43.03047 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:25:43.065996 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:25:43.127209 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:25:53.145194 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:25:53.207567 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:25:53.270056 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:25:53.288322 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:25:53.31691 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:25:53.379726 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:25:53.38449 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:25:53.395039 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:25:53.47678 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:25:53.482081 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:25:53.526269 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:25:53.562702 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:25:53.573913 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:25:53.618292 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:25:53.689203 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:26:13.18979 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:26:21.350368 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:26:41.129621 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:26:49.412855 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:26:49.899979 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_linear.rds
2025-11-18 03:26:49.945842 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_linear.rds
2025-11-18 03:26:49.974659 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_logistic.rds
2025-11-18 03:26:50.026637 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_logistic.rds
2025-11-18 03:27:08.924527 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:27:14.171282 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:27:14.426087 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_linear.rds
2025-11-18 03:27:14.473278 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_linear.rds
2025-11-18 03:27:14.503121 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_logistic.rds
2025-11-18 03:27:14.553722 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_logistic.rds
2025-11-18 03:27:29.369571 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:27:34.697178 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 03:27:35.009579 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_linear.rds
2025-11-18 03:27:35.059843 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_linear.rds
2025-11-18 03:27:35.08978 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_logistic.rds
2025-11-18 03:27:35.142971 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_logistic.rds
2025-11-18 03:27:49.677051 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:27:49.776443 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:27:49.84321 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:27:49.862331 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:27:49.890748 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:27:49.955027 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:27:49.959849 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:27:49.970179 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:27:50.074108 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:27:50.078838 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:27:50.119945 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:27:50.153582 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:27:50.169125 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:27:50.203118 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:27:50.258534 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:27:59.647761 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 03:27:59.701708 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 03:27:59.755611 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 03:27:59.771352 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 03:27:59.795765 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 03:27:59.851148 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 03:27:59.855529 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 03:27:59.864924 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 03:27:59.941612 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 03:27:59.946018 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 03:27:59.987351 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 03:28:00.019797 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 03:28:00.029727 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 03:28:00.065522 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 03:28:00.122299 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 03:28:00.353051 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_linear.rds
2025-11-18 03:28:00.39362 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_linear.rds
2025-11-18 03:28:00.436795 WARNING::Deleting existing residuals file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/residuals_logistic.rds
2025-11-18 03:28:00.653633 WARNING::Deleting existing fitted file: /tmp/Rtmpg7LGaq/file35d17fdddb6/fits/fitted_logistic.rds
2025-11-18 03:28:15.33119 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-18 03:28:15.343245 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-18 03:28:15.351327 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-18 03:28:15.390846 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-11-18 03:28:15.403629 ERROR::Effect name not found in metadata: d
2025-11-18 03:28:15.412207 ERROR::No user formula provided
2025-11-18 03:28:15.437299 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-18 03:28:15.446598 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-11-18 03:28:17.525138 INFO::Writing function arguments to log file
2025-11-18 03:28:17.542211 INFO::Verifying options selected are valid
2025-11-18 03:28:19.19329 INFO::Writing function arguments to log file
2025-11-18 03:28:19.207514 INFO::Verifying options selected are valid
2025-11-18 03:28:19.208463 INFO::Determining format of input files
2025-11-18 03:28:19.209309 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 03:28:19.211411 INFO::Running selected normalization method: TSS
2025-11-18 03:28:19.212615 INFO::Creating output feature tables folder
2025-11-18 03:28:19.213537 INFO::Writing normalized data to file /tmp/Rtmpg7LGaq/file35d15055307e/features/data_norm.tsv
2025-11-18 03:28:19.215005 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-18 03:28:19.21582 INFO::Total samples in data: 16
2025-11-18 03:28:19.216584 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-18 03:28:19.21737 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-18 03:28:19.218945 INFO::Total filtered features: 0
2025-11-18 03:28:19.219768 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-18 03:28:19.220791 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-18 03:28:19.221748 INFO::Filtered feature names from variance filtering:
2025-11-18 03:28:19.222644 INFO::Writing filtered data to file /tmp/Rtmpg7LGaq/file35d15055307e/features/filtered_data.tsv
2025-11-18 03:28:19.224054 INFO::Running selected transform method: LOG
2025-11-18 03:28:19.225063 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpg7LGaq/file35d15055307e/features/data_transformed.tsv
2025-11-18 03:28:19.226567 INFO::Applying z-score to standardize continuous metadata
2025-11-18 03:28:19.230607 INFO::Running the linear model component
2025-11-18 03:28:19.245288 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:19.249191 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:19.25251 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:19.257793 INFO::Counting total values for each feature
2025-11-18 03:28:19.259245 INFO::Running the logistic model component
2025-11-18 03:28:19.273555 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:19.278515 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:19.283092 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:19.289685 INFO::Counting total values for each feature
2025-11-18 03:28:19.291436 INFO::Re-running abundances for warn_prevalence
2025-11-18 03:28:19.292299 INFO::Running selected normalization method: TSS
2025-11-18 03:28:19.293551 INFO::Running selected transform method: LOG
2025-11-18 03:28:19.308335 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:19.311785 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:19.314913 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:19.376784 INFO::Creating fits folder
2025-11-18 03:28:19.378033 INFO::Writing residuals to file /tmp/Rtmpg7LGaq/file35d15055307e/fits/residuals_linear.rds
2025-11-18 03:28:19.379254 INFO::Writing fitted values to file /tmp/Rtmpg7LGaq/file35d15055307e/fits/fitted_linear.rds
2025-11-18 03:28:19.380366 INFO::Writing residuals to file /tmp/Rtmpg7LGaq/file35d15055307e/fits/residuals_logistic.rds
2025-11-18 03:28:19.381536 INFO::Writing fitted values to file /tmp/Rtmpg7LGaq/file35d15055307e/fits/fitted_logistic.rds
2025-11-18 03:28:19.383673 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmpg7LGaq/file35d15055307e/all_results.tsv
2025-11-18 03:28:19.385188 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/Rtmpg7LGaq/file35d15055307e/significant_results.tsv
2025-11-18 03:28:19.386488 INFO::Creating output figures folder
2025-11-18 03:28:19.387674 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmpg7LGaq/file35d15055307e/figures/summary_plot.pdf
2025-11-18 03:28:20.482406 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpg7LGaq/file35d15055307e/figures
2025-11-18 03:28:20.483953 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 03:28:20.487809 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 03:28:20.839887 INFO::Writing summary plot of
                        significant results to file: /tmp/Rtmpg7LGaq/file35d15055307e/figures/summary_plot.pdf
2025-11-18 03:28:21.923801 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpg7LGaq/file35d15055307e/figures
2025-11-18 03:28:21.924881 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 03:28:21.928297 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 03:28:22.2737 INFO::Running the linear model component
2025-11-18 03:28:22.279599 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:22.282737 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:22.28577 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:22.290809 INFO::Counting total values for each feature
2025-11-18 03:28:22.292083 INFO::Running the logistic model component
2025-11-18 03:28:22.298175 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:22.302369 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:22.306425 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:22.312504 INFO::Counting total values for each feature
2025-11-18 03:28:22.313812 INFO::Re-running abundances for warn_prevalence
2025-11-18 03:28:22.314337 INFO::Running selected normalization method: TSS
2025-11-18 03:28:22.315485 INFO::Running selected transform method: LOG
2025-11-18 03:28:22.32142 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:22.324239 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:22.327471 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:22.38881 INFO::Creating output folder
2025-11-18 03:28:22.389669 INFO::Creating output figures folder
2025-11-18 03:28:22.39071 INFO::Writing summary plot of significant
                        results to file: /tmp/Rtmpg7LGaq/file35d17b8fed72/figures/summary_plot.pdf
2025-11-18 03:28:23.477209 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpg7LGaq/file35d17b8fed72/figures
2025-11-18 03:28:23.478365 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 03:28:23.481938 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 03:28:24.204194 INFO::Applying z-score to standardize continuous metadata
2025-11-18 03:28:24.210366 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-18 03:28:24.211037 INFO::Bypass z-score application to metadata
2025-11-18 03:28:24.212931 INFO::Bypass z-score application to metadata
2025-11-18 03:28:24.229232 INFO::Determining format of input files
2025-11-18 03:28:24.229941 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 03:28:24.230598 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-18 03:28:24.235913 INFO::Determining format of input files
2025-11-18 03:28:24.236645 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-18 03:28:24.237558 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 03:28:24.243236 INFO::Determining format of input files
2025-11-18 03:28:24.243935 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 03:28:24.244671 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 03:28:24.245797 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-18 03:28:24.246347 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-18 03:28:24.255117 INFO::Running selected transform method: LOG
2025-11-18 03:28:24.256017 INFO::Creating output feature tables folder
2025-11-18 03:28:24.256842 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpg7LGaq/file35d14a641e58/features/data_transformed.tsv
2025-11-18 03:28:24.259976 INFO::Running selected transform method: LOG
2025-11-18 03:28:24.260709 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpg7LGaq/file35d14a641e58/features/data_transformed.tsv
2025-11-18 03:28:24.263459 INFO::Running selected transform method: PLOG
2025-11-18 03:28:24.264555 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpg7LGaq/file35d14a641e58/features/data_transformed.tsv
2025-11-18 03:28:24.266764 INFO::Running selected transform method: NONE
2025-11-18 03:28:24.267316 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpg7LGaq/file35d14a641e58/features/data_transformed.tsv
2025-11-18 03:28:24.274916 INFO::Running the linear model component
2025-11-18 03:28:24.280851 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:24.283925 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:24.286708 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:24.291649 INFO::Counting total values for each feature
2025-11-18 03:28:24.292846 INFO::Running the logistic model component
2025-11-18 03:28:24.298668 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:24.303028 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:24.307385 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:24.313775 INFO::Counting total values for each feature
2025-11-18 03:28:24.315255 INFO::Re-running abundances for warn_prevalence
2025-11-18 03:28:24.315857 INFO::Running selected normalization method: TSS
2025-11-18 03:28:24.31687 INFO::Running selected transform method: LOG
2025-11-18 03:28:24.322942 INFO::Fitting model to feature number 1, a
2025-11-18 03:28:24.325998 INFO::Fitting model to feature number 2, b
2025-11-18 03:28:24.328939 INFO::Fitting model to feature number 3, c
2025-11-18 03:28:24.391512 INFO::Creating output folder
2025-11-18 03:28:24.392415 INFO::Creating fits folder
2025-11-18 03:28:24.393175 INFO::Writing residuals to file /tmp/Rtmpg7LGaq/file35d17304498f/fits/residuals_linear.rds
2025-11-18 03:28:24.394126 INFO::Writing fitted values to file /tmp/Rtmpg7LGaq/file35d17304498f/fits/fitted_linear.rds
2025-11-18 03:28:24.395007 INFO::Writing residuals to file /tmp/Rtmpg7LGaq/file35d17304498f/fits/residuals_logistic.rds
2025-11-18 03:28:24.395883 INFO::Writing fitted values to file /tmp/Rtmpg7LGaq/file35d17304498f/fits/fitted_logistic.rds
2025-11-18 03:28:24.397813 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/Rtmpg7LGaq/file35d17304498f/all_results.tsv
2025-11-18 03:28:24.399118 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/Rtmpg7LGaq/file35d17304498f/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
281.080   7.260 289.133

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin314.898 0.90815.835
maaslin_check_arguments0.1260.0030.130
maaslin_check_formula0.1410.0180.158
maaslin_compute_formula0.1300.0090.139
maaslin_contrast_test15.202 1.26616.556
maaslin_filter0.4560.0480.508
maaslin_fit10.121 0.82810.986
maaslin_log_arguments0.1080.0070.117
maaslin_normalize0.2340.0150.251
maaslin_plot_results33.527 0.92734.668
maaslin_plot_results_from_output35.038 1.29036.660
maaslin_process_metadata0.4360.0240.464
maaslin_read_data0.1060.0070.115
maaslin_reorder_data0.1130.0070.122
maaslin_transform0.5590.0420.604
maaslin_write_results10.674 0.78711.497
maaslin_write_results_lefse_format11.730 0.55712.325
preprocess_dna_mtx0.0040.0010.004
preprocess_taxa_mtx0.0040.0000.005