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 12:10 -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 kjohnson3

To the developers/maintainers of the maaslin3 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maaslin3.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: maaslin3
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.1.0.tar.gz
StartedAt: 2025-08-08 20:04:45 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:09:12 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 267.3 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 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.1.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maaslin3’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
maaslin_plot_results_from_output   13.910  0.624  14.638
maaslin_plot_results               13.534  0.667  14.261
maaslin3                            8.259  0.502   8.781
maaslin_contrast_test               7.164  0.631   7.826
maaslin_write_results_lefse_format  5.686  0.338   6.063
maaslin_write_results               5.326  0.529   5.884
maaslin_fit                         4.897  0.572   5.493
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘maaslin3’ ...
** this is package ‘maaslin3’ version ‘1.1.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maaslin3)

Tests output

maaslin3.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> library(testthat)
> library(maaslin3)
> 
> test_check("maaslin3")
2025-08-08 20:07:06.492572 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:06.517562 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:06.544885 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:06.552103 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:06.567346 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:06.59185 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:06.593754 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:06.59764 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:06.633389 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:06.635373 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:06.657264 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:06.671436 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:06.675823 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:06.689708 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:06.717775 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:13.229455 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:13.256341 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:13.282682 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:13.29033 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:13.302447 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:13.329986 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:13.343005 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:13.347227 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:13.380961 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:13.383555 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:13.401876 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:13.416638 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:13.421075 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:13.435419 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:13.460049 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:14.650 R[93223:490474032] XType: Using static font registry.
2025-08-08 20:07:20.810836 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:20.848415 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:20.875109 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:20.882986 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:20.895199 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:20.922576 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:20.924681 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:20.929096 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:20.964719 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:20.966991 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:21.015422 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:21.030282 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:21.034618 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:21.048793 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:21.073143 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:26.579738 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:26.607132 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:26.635458 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:26.643274 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:26.655307 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:26.682353 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:26.684437 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:26.688705 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:26.724749 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:26.72693 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:26.746206 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:26.761927 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:26.766778 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:26.783219 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:26.809629 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:26.901392 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/residuals_linear.rds
2025-08-08 20:07:26.933461 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/fitted_linear.rds
2025-08-08 20:07:26.966674 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/residuals_logistic.rds
2025-08-08 20:07:27.133048 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/fitted_logistic.rds
2025-08-08 20:07:33.683922 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:33.709452 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:33.735583 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:33.742561 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:33.753478 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:33.777688 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:33.779524 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:33.783271 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:33.814029 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:33.816005 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:33.832652 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:33.845234 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:33.849324 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:33.862263 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:33.884173 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:39.329934 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:39.356316 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:39.381781 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:39.389374 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:39.40139 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:39.427544 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:39.429556 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:39.433675 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:39.467382 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:39.46947 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:39.48898 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:39.504871 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:39.509555 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:39.524494 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:39.550492 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:39.632255 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/residuals_linear.rds
2025-08-08 20:07:39.665126 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/fitted_linear.rds
2025-08-08 20:07:39.698381 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/residuals_logistic.rds
2025-08-08 20:07:39.865235 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/fitted_logistic.rds
2025-08-08 20:07:46.374707 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:46.401965 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:46.428237 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:46.43608 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:46.448067 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:46.474706 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:46.476971 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:46.481296 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:46.515293 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:46.517355 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:46.533714 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:46.547063 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:46.55115 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:46.584269 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:46.606788 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:51.378797 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:51.40565 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:51.431521 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:51.439057 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:51.450776 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:51.477088 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:51.479375 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:51.483862 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:51.519622 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:51.522031 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:51.540708 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:51.554988 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:51.559558 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:51.575412 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:51.601134 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:07:51.696062 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/residuals_linear.rds
2025-08-08 20:07:51.728613 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/fitted_linear.rds
2025-08-08 20:07:51.761903 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/residuals_logistic.rds
2025-08-08 20:07:51.930048 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27573b8c9a/fits/fitted_logistic.rds
2025-08-08 20:07:58.281514 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:07:58.310987 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:07:58.33739 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:07:58.345246 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:07:58.35728 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:07:58.384154 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:07:58.386197 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:07:58.390318 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:07:58.445885 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:07:58.448056 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:07:58.464766 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:07:58.478427 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:07:58.48269 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:07:58.496439 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:07:58.52003 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:08:03.484938 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:08:03.5313 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:08:03.556211 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:08:03.563815 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:08:03.575287 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:08:03.600675 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:08:03.602677 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:08:03.60674 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:08:03.639363 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:08:03.641459 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:08:03.658163 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:08:03.671828 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:08:03.676009 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:08:03.689551 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:08:03.713606 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:08:11.094447 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:15.013899 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:22.790231 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:26.669483 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:26.905517 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_linear.rds
2025-08-08 20:08:26.939005 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_linear.rds
2025-08-08 20:08:26.961055 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_logistic.rds
2025-08-08 20:08:27.001428 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_logistic.rds
2025-08-08 20:08:34.234016 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:36.905806 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:37.005476 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_linear.rds
2025-08-08 20:08:37.038318 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_linear.rds
2025-08-08 20:08:37.060588 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_logistic.rds
2025-08-08 20:08:37.101496 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_logistic.rds
2025-08-08 20:08:43.585898 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:45.779473 WARNING::Fitting problem for feature 124 returning NA
2025-08-08 20:08:45.901323 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_linear.rds
2025-08-08 20:08:45.934048 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_linear.rds
2025-08-08 20:08:45.95597 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_logistic.rds
2025-08-08 20:08:45.996158 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_logistic.rds
2025-08-08 20:08:51.846444 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:08:51.872379 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:08:51.897754 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:08:51.905505 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:08:51.917591 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:08:51.94489 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:08:51.946958 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:08:51.951232 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:08:51.984885 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:08:51.986975 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:08:52.004105 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:08:52.018145 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:08:52.02248 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:08:52.059224 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:08:52.084115 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:08:57.167365 WARNING::Fitting problem for feature 50 returning NA
2025-08-08 20:08:57.194105 WARNING::Fitting problem for feature 62 returning NA
2025-08-08 20:08:57.221422 WARNING::Fitting problem for feature 74 returning NA
2025-08-08 20:08:57.229647 WARNING::Fitting problem for feature 78 returning NA
2025-08-08 20:08:57.242278 WARNING::Fitting problem for feature 84 returning NA
2025-08-08 20:08:57.268184 WARNING::Fitting problem for feature 96 returning NA
2025-08-08 20:08:57.270174 WARNING::Fitting problem for feature 97 returning NA
2025-08-08 20:08:57.274242 WARNING::Fitting problem for feature 99 returning NA
2025-08-08 20:08:57.306789 WARNING::Fitting problem for feature 114 returning NA
2025-08-08 20:08:57.308855 WARNING::Fitting problem for feature 115 returning NA
2025-08-08 20:08:57.326181 WARNING::Fitting problem for feature 123 returning NA
2025-08-08 20:08:57.341443 WARNING::Fitting problem for feature 130 returning NA
2025-08-08 20:08:57.345607 WARNING::Fitting problem for feature 132 returning NA
2025-08-08 20:08:57.359909 WARNING::Fitting problem for feature 139 returning NA
2025-08-08 20:08:57.383658 WARNING::Fitting problem for feature 150 returning NA
2025-08-08 20:08:57.474222 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_linear.rds
2025-08-08 20:08:57.511207 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_linear.rds
2025-08-08 20:08:57.547259 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/residuals_logistic.rds
2025-08-08 20:08:57.71911 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27158a234/fits/fitted_logistic.rds
2025-08-08 20:09:03.953891 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-08 20:09:03.959283 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-08 20:09:03.962939 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-08 20:09:03.979021 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-08 20:09:03.984124 ERROR::Effect name not found in metadata: d
2025-08-08 20:09:03.987505 ERROR::No user formula provided
2025-08-08 20:09:03.996725 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-08 20:09:04.000411 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-08 20:09:04.996061 INFO::Writing function arguments to log file
2025-08-08 20:09:05.001232 INFO::Verifying options selected are valid
2025-08-08 20:09:05.688395 INFO::Writing function arguments to log file
2025-08-08 20:09:05.692967 INFO::Verifying options selected are valid
2025-08-08 20:09:05.693357 INFO::Determining format of input files
2025-08-08 20:09:05.693675 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 20:09:05.694496 INFO::Running selected normalization method: TSS
2025-08-08 20:09:05.694994 INFO::Creating output feature tables folder
2025-08-08 20:09:05.695393 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/features/data_norm.tsv
2025-08-08 20:09:05.695992 INFO::Filter data based on min abundance and min prevalence
2025-08-08 20:09:05.696296 INFO::Total samples in data: 16
2025-08-08 20:09:05.696586 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-08 20:09:05.697186 INFO::Total filtered features: 0
2025-08-08 20:09:05.697516 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-08 20:09:05.697891 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-08 20:09:05.698199 INFO::Filtered feature names from variance filtering:
2025-08-08 20:09:05.698492 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/features/filtered_data.tsv
2025-08-08 20:09:05.699059 INFO::Running selected transform method: LOG
2025-08-08 20:09:05.699446 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/features/data_transformed.tsv
2025-08-08 20:09:05.700038 INFO::Applying z-score to standardize continuous metadata
2025-08-08 20:09:05.701932 INFO::Running the linear model component
2025-08-08 20:09:05.707134 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:05.708597 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:05.709907 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:05.712225 INFO::Counting total values for each feature
2025-08-08 20:09:05.712875 INFO::Running the logistic model component
2025-08-08 20:09:05.718055 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:05.720096 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:05.721947 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:05.724705 INFO::Counting total values for each feature
2025-08-08 20:09:05.725462 INFO::Re-running abundances for warn_prevalence
2025-08-08 20:09:05.725787 INFO::Running selected normalization method: TSS
2025-08-08 20:09:05.726288 INFO::Running selected transform method: LOG
2025-08-08 20:09:05.731349 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:05.732741 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:05.734014 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:05.760688 INFO::Creating fits folder
2025-08-08 20:09:05.761226 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/fits/residuals_linear.rds
2025-08-08 20:09:05.76177 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/fits/fitted_linear.rds
2025-08-08 20:09:05.76226 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/fits/residuals_logistic.rds
2025-08-08 20:09:05.762739 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/fits/fitted_logistic.rds
2025-08-08 20:09:05.763744 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/all_results.tsv
2025-08-08 20:09:05.764389 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/significant_results.tsv
2025-08-08 20:09:05.764964 INFO::Creating output figures folder
2025-08-08 20:09:05.765444 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/figures/summary_plot.pdf
2025-08-08 20:09:06.236952 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/figures
2025-08-08 20:09:06.237743 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 20:09:06.239665 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 20:09:06.3906 INFO::Writing summary plot of
                        significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/figures/summary_plot.pdf
2025-08-08 20:09:06.862557 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2710401b5a/figures
2025-08-08 20:09:06.863107 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 20:09:06.864842 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 20:09:07.011354 INFO::Running the linear model component
2025-08-08 20:09:07.014066 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:07.015467 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:07.016648 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:07.018924 INFO::Counting total values for each feature
2025-08-08 20:09:07.019466 INFO::Running the logistic model component
2025-08-08 20:09:07.021932 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:07.023851 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:07.025573 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:07.028479 INFO::Counting total values for each feature
2025-08-08 20:09:07.029204 INFO::Re-running abundances for warn_prevalence
2025-08-08 20:09:07.029449 INFO::Running selected normalization method: TSS
2025-08-08 20:09:07.029891 INFO::Running selected transform method: LOG
2025-08-08 20:09:07.032561 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:07.033977 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:07.035212 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:07.061928 INFO::Creating output folder
2025-08-08 20:09:07.062344 INFO::Creating output figures folder
2025-08-08 20:09:07.062756 INFO::Writing summary plot of significant
                        results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2732550d66/figures/summary_plot.pdf
2025-08-08 20:09:07.532182 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c2732550d66/figures
2025-08-08 20:09:07.532756 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-08 20:09:07.534513 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-08 20:09:07.875369 INFO::Applying z-score to standardize continuous metadata
2025-08-08 20:09:07.877931 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-08 20:09:07.878185 INFO::Bypass z-score application to metadata
2025-08-08 20:09:07.878892 INFO::Bypass z-score application to metadata
2025-08-08 20:09:07.88485 INFO::Determining format of input files
2025-08-08 20:09:07.885143 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 20:09:07.885384 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-08 20:09:07.887424 INFO::Determining format of input files
2025-08-08 20:09:07.887733 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-08 20:09:07.888109 INFO::Input format is feature_specific_covariate samples as columns
2025-08-08 20:09:07.890442 INFO::Determining format of input files
2025-08-08 20:09:07.890745 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-08 20:09:07.891056 INFO::Input format is feature_specific_covariate samples as columns
2025-08-08 20:09:07.891509 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 20:09:07.891717 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 20:09:07.895118 INFO::Running selected transform method: LOG
2025-08-08 20:09:07.895465 INFO::Creating output feature tables folder
2025-08-08 20:09:07.895822 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27490ae713/features/data_transformed.tsv
2025-08-08 20:09:07.897052 INFO::Running selected transform method: LOG
2025-08-08 20:09:07.897357 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27490ae713/features/data_transformed.tsv
2025-08-08 20:09:07.89845 INFO::Running selected transform method: PLOG
2025-08-08 20:09:07.898917 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27490ae713/features/data_transformed.tsv
2025-08-08 20:09:07.899755 INFO::Running selected transform method: NONE
2025-08-08 20:09:07.899981 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c27490ae713/features/data_transformed.tsv
2025-08-08 20:09:07.90241 INFO::Running the linear model component
2025-08-08 20:09:07.904954 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:07.906294 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:07.907455 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:07.909706 INFO::Counting total values for each feature
2025-08-08 20:09:07.910243 INFO::Running the logistic model component
2025-08-08 20:09:07.912767 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:07.914681 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:07.916431 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:07.919102 INFO::Counting total values for each feature
2025-08-08 20:09:07.919741 INFO::Re-running abundances for warn_prevalence
2025-08-08 20:09:07.919966 INFO::Running selected normalization method: TSS
2025-08-08 20:09:07.920361 INFO::Running selected transform method: LOG
2025-08-08 20:09:07.922898 INFO::Fitting model to feature number 1, a
2025-08-08 20:09:07.924106 INFO::Fitting model to feature number 2, b
2025-08-08 20:09:07.925242 INFO::Fitting model to feature number 3, c
2025-08-08 20:09:07.951389 INFO::Creating output folder
2025-08-08 20:09:07.951774 INFO::Creating fits folder
2025-08-08 20:09:07.952062 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c276ac8b5db/fits/residuals_linear.rds
2025-08-08 20:09:07.952432 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c276ac8b5db/fits/fitted_linear.rds
2025-08-08 20:09:07.952761 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c276ac8b5db/fits/residuals_logistic.rds
2025-08-08 20:09:07.953097 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c276ac8b5db/fits/fitted_logistic.rds
2025-08-08 20:09:07.953906 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c276ac8b5db/all_results.tsv
2025-08-08 20:09:07.954459 INFO::Writing the significant results without errors (those which have joint q-values less than or equal to the threshold of 0.100000 ) to file (ordered by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpdjjrJM/file16c276ac8b5db/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
120.233   5.309 126.093

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin38.2590.5028.781
maaslin_check_arguments0.0590.0020.061
maaslin_check_formula0.0560.0040.061
maaslin_compute_formula0.0560.0030.059
maaslin_contrast_test7.1640.6317.826
maaslin_filter0.2190.0240.248
maaslin_fit4.8970.5725.493
maaslin_log_arguments0.0530.0020.055
maaslin_normalize0.1210.0090.132
maaslin_plot_results13.534 0.66714.261
maaslin_plot_results_from_output13.910 0.62414.638
maaslin_process_metadata0.2250.0140.240
maaslin_read_data0.0520.0030.055
maaslin_reorder_data0.0550.0040.060
maaslin_transform0.2710.0230.294
maaslin_write_results5.3260.5295.884
maaslin_write_results_lefse_format5.6860.3386.063
preprocess_dna_mtx0.0010.0000.002
preprocess_taxa_mtx0.0020.0000.001