Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-18 13:40 -0400 (Mon, 18 Aug 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.0.tar.gz
StartedAt: 2025-08-20 23:52:28 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-21 00:11:56 -0400 (Thu, 21 Aug 2025)
EllapsedTime: 1167.5 seconds
RetCode: 0
Status:   OK  
CheckDir: maaslin3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings maaslin3_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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               36.438  0.527  36.928
maaslin_plot_results_from_output   35.478  0.341  35.821
maaslin_contrast_test              19.193  0.632  19.827
maaslin3                           19.035  0.626  19.666
maaslin_write_results_lefse_format 14.989  0.094  15.084
maaslin_write_results              13.440  0.282  13.722
maaslin_fit                        13.434  0.089  13.524
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

maaslin3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL maaslin3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
2025-08-20 23:58:23.606294 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 23:58:23.680576 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 23:58:23.763915 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 23:58:23.785074 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 23:58:23.826783 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 23:58:23.90354 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 23:58:23.90906 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 23:58:23.920978 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 23:58:24.020477 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 23:58:24.025657 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 23:58:24.073035 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 23:58:24.111965 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 23:58:24.123324 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 23:58:24.162439 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 23:58:24.238078 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 23:58:40.096171 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 23:58:40.170665 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 23:58:40.24563 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 23:58:40.269238 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 23:58:40.306641 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 23:58:40.390987 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 23:58:40.397278 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 23:58:40.411728 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 23:58:40.537276 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 23:58:40.542637 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 23:58:40.59148 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 23:58:40.63122 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 23:58:40.642786 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 23:58:40.682102 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 23:58:40.751952 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 23:58:59.225609 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 23:58:59.316391 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 23:58:59.391214 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 23:58:59.412899 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 23:58:59.447178 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 23:58:59.521933 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 23:58:59.527439 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 23:58:59.539408 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 23:58:59.636693 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 23:58:59.642576 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 23:58:59.722344 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 23:58:59.768061 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 23:58:59.780204 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 23:58:59.820195 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 23:58:59.887449 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 23:59:12.951433 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 23:59:13.028879 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 23:59:13.10154 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 23:59:13.122445 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 23:59:13.155724 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 23:59:13.228994 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 23:59:13.234331 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 23:59:13.245771 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 23:59:13.336204 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 23:59:13.34151 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 23:59:13.390324 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 23:59:13.430301 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 23:59:13.442074 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 23:59:13.48265 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 23:59:13.550964 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 23:59:13.783867 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_linear.rds
2025-08-20 23:59:13.846273 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_linear.rds
2025-08-20 23:59:13.910379 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_logistic.rds
2025-08-20 23:59:14.211494 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_logistic.rds
2025-08-20 23:59:30.82741 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 23:59:30.926561 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 23:59:31.004512 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 23:59:31.027686 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 23:59:31.064569 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 23:59:31.144409 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 23:59:31.150118 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 23:59:31.162783 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 23:59:31.261139 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 23:59:31.266773 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 23:59:31.316768 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 23:59:31.356505 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 23:59:31.368094 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 23:59:31.407008 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 23:59:31.475543 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 23:59:44.151783 WARNING::Fitting problem for feature 50 returning NA
2025-08-20 23:59:44.226765 WARNING::Fitting problem for feature 62 returning NA
2025-08-20 23:59:44.30115 WARNING::Fitting problem for feature 74 returning NA
2025-08-20 23:59:44.323188 WARNING::Fitting problem for feature 78 returning NA
2025-08-20 23:59:44.357823 WARNING::Fitting problem for feature 84 returning NA
2025-08-20 23:59:44.43394 WARNING::Fitting problem for feature 96 returning NA
2025-08-20 23:59:44.439843 WARNING::Fitting problem for feature 97 returning NA
2025-08-20 23:59:44.452338 WARNING::Fitting problem for feature 99 returning NA
2025-08-20 23:59:44.548516 WARNING::Fitting problem for feature 114 returning NA
2025-08-20 23:59:44.553979 WARNING::Fitting problem for feature 115 returning NA
2025-08-20 23:59:44.60408 WARNING::Fitting problem for feature 123 returning NA
2025-08-20 23:59:44.645165 WARNING::Fitting problem for feature 130 returning NA
2025-08-20 23:59:44.658923 WARNING::Fitting problem for feature 132 returning NA
2025-08-20 23:59:44.701982 WARNING::Fitting problem for feature 139 returning NA
2025-08-20 23:59:44.774384 WARNING::Fitting problem for feature 150 returning NA
2025-08-20 23:59:44.984754 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_linear.rds
2025-08-20 23:59:45.045456 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_linear.rds
2025-08-20 23:59:45.108271 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_logistic.rds
2025-08-20 23:59:45.409223 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_logistic.rds
2025-08-21 00:00:02.167132 WARNING::Fitting problem for feature 50 returning NA
2025-08-21 00:00:02.243215 WARNING::Fitting problem for feature 62 returning NA
2025-08-21 00:00:02.318333 WARNING::Fitting problem for feature 74 returning NA
2025-08-21 00:00:02.340014 WARNING::Fitting problem for feature 78 returning NA
2025-08-21 00:00:02.374471 WARNING::Fitting problem for feature 84 returning NA
2025-08-21 00:00:02.452549 WARNING::Fitting problem for feature 96 returning NA
2025-08-21 00:00:02.458198 WARNING::Fitting problem for feature 97 returning NA
2025-08-21 00:00:02.470507 WARNING::Fitting problem for feature 99 returning NA
2025-08-21 00:00:02.569526 WARNING::Fitting problem for feature 114 returning NA
2025-08-21 00:00:02.575295 WARNING::Fitting problem for feature 115 returning NA
2025-08-21 00:00:02.62837 WARNING::Fitting problem for feature 123 returning NA
2025-08-21 00:00:02.671816 WARNING::Fitting problem for feature 130 returning NA
2025-08-21 00:00:02.684543 WARNING::Fitting problem for feature 132 returning NA
2025-08-21 00:00:02.726545 WARNING::Fitting problem for feature 139 returning NA
2025-08-21 00:00:02.811038 WARNING::Fitting problem for feature 150 returning NA
2025-08-21 00:00:14.869803 WARNING::Fitting problem for feature 50 returning NA
2025-08-21 00:00:14.947856 WARNING::Fitting problem for feature 62 returning NA
2025-08-21 00:00:15.025149 WARNING::Fitting problem for feature 74 returning NA
2025-08-21 00:00:15.046834 WARNING::Fitting problem for feature 78 returning NA
2025-08-21 00:00:15.080911 WARNING::Fitting problem for feature 84 returning NA
2025-08-21 00:00:15.157269 WARNING::Fitting problem for feature 96 returning NA
2025-08-21 00:00:15.162816 WARNING::Fitting problem for feature 97 returning NA
2025-08-21 00:00:15.174966 WARNING::Fitting problem for feature 99 returning NA
2025-08-21 00:00:15.27034 WARNING::Fitting problem for feature 114 returning NA
2025-08-21 00:00:15.275722 WARNING::Fitting problem for feature 115 returning NA
2025-08-21 00:00:15.325745 WARNING::Fitting problem for feature 123 returning NA
2025-08-21 00:00:15.368392 WARNING::Fitting problem for feature 130 returning NA
2025-08-21 00:00:15.381969 WARNING::Fitting problem for feature 132 returning NA
2025-08-21 00:00:15.424185 WARNING::Fitting problem for feature 139 returning NA
2025-08-21 00:00:15.496599 WARNING::Fitting problem for feature 150 returning NA
2025-08-21 00:00:15.704002 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_linear.rds
2025-08-21 00:00:15.765436 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_linear.rds
2025-08-21 00:00:15.829647 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/residuals_logistic.rds
2025-08-21 00:00:16.132642 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f418373399cac/fits/fitted_logistic.rds
2025-08-21 00:00:32.775272 WARNING::Fitting problem for feature 50 returning NA
2025-08-21 00:00:32.850307 WARNING::Fitting problem for feature 62 returning NA
2025-08-21 00:00:32.925143 WARNING::Fitting problem for feature 74 returning NA
2025-08-21 00:00:32.94694 WARNING::Fitting problem for feature 78 returning NA
2025-08-21 00:00:32.981642 WARNING::Fitting problem for feature 84 returning NA
2025-08-21 00:00:33.057997 WARNING::Fitting problem for feature 96 returning NA
2025-08-21 00:00:33.063529 WARNING::Fitting problem for feature 97 returning NA
2025-08-21 00:00:33.075543 WARNING::Fitting problem for feature 99 returning NA
2025-08-21 00:00:33.171884 WARNING::Fitting problem for feature 114 returning NA
2025-08-21 00:00:33.177451 WARNING::Fitting problem for feature 115 returning NA
2025-08-21 00:00:33.228448 WARNING::Fitting problem for feature 123 returning NA
2025-08-21 00:00:33.269985 WARNING::Fitting problem for feature 130 returning NA
2025-08-21 00:00:33.282526 WARNING::Fitting problem for feature 132 returning NA
2025-08-21 00:00:33.323844 WARNING::Fitting problem for feature 139 returning NA
2025-08-21 00:00:33.393555 WARNING::Fitting problem for feature 150 returning NA
2025-08-21 00:00:45.200852 WARNING::Fitting problem for feature 50 returning NA
2025-08-21 00:00:45.279269 WARNING::Fitting problem for feature 62 returning NA
2025-08-21 00:00:45.354671 WARNING::Fitting problem for feature 74 returning NA
2025-08-21 00:00:45.376484 WARNING::Fitting problem for feature 78 returning NA
2025-08-21 00:00:45.41076 WARNING::Fitting problem for feature 84 returning NA
2025-08-21 00:00:45.486995 WARNING::Fitting problem for feature 96 returning NA
2025-08-21 00:00:45.492499 WARNING::Fitting problem for feature 97 returning NA
2025-08-21 00:00:45.504451 WARNING::Fitting problem for feature 99 returning NA
2025-08-21 00:00:45.600658 WARNING::Fitting problem for feature 114 returning NA
2025-08-21 00:00:45.60603 WARNING::Fitting problem for feature 115 returning NA
2025-08-21 00:00:45.655805 WARNING::Fitting problem for feature 123 returning NA
2025-08-21 00:00:45.697776 WARNING::Fitting problem for feature 130 returning NA
2025-08-21 00:00:45.710458 WARNING::Fitting problem for feature 132 returning NA
2025-08-21 00:00:45.751664 WARNING::Fitting problem for feature 139 returning NA
2025-08-21 00:00:45.82053 WARNING::Fitting problem for feature 150 returning NA
2025-08-21 00:01:04.485921 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:01:14.289268 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:01:33.958329 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:01:43.336162 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:01:43.987976 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds
2025-08-21 00:01:44.049304 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds
2025-08-21 00:01:44.087703 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds
2025-08-21 00:01:44.155739 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds
2025-08-21 00:02:02.044698 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:02:07.374391 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:02:07.707165 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds
2025-08-21 00:02:07.769219 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds
2025-08-21 00:02:07.807769 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds
2025-08-21 00:02:07.876359 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds
2025-08-21 00:02:23.521142 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:02:28.588792 WARNING::Fitting problem for feature 124 returning NA
2025-08-21 00:02:28.899455 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds
2025-08-21 00:02:28.960909 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds
2025-08-21 00:02:29.000312 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds
2025-08-21 00:02:29.069989 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds
2025-08-21 00:02:44.416397 WARNING::Fitting problem for feature 50 returning NA
2025-08-21 00:02:44.494793 WARNING::Fitting problem for feature 62 returning NA
2025-08-21 00:02:44.570112 WARNING::Fitting problem for feature 74 returning NA
2025-08-21 00:02:44.59284 WARNING::Fitting problem for feature 78 returning NA
2025-08-21 00:02:44.636932 WARNING::Fitting problem for feature 84 returning NA
2025-08-21 00:02:44.713373 WARNING::Fitting problem for feature 96 returning NA
2025-08-21 00:02:44.718697 WARNING::Fitting problem for feature 97 returning NA
2025-08-21 00:02:44.730484 WARNING::Fitting problem for feature 99 returning NA
2025-08-21 00:02:44.827604 WARNING::Fitting problem for feature 114 returning NA
2025-08-21 00:02:44.833278 WARNING::Fitting problem for feature 115 returning NA
2025-08-21 00:02:44.885157 WARNING::Fitting problem for feature 123 returning NA
2025-08-21 00:02:44.926008 WARNING::Fitting problem for feature 130 returning NA
2025-08-21 00:02:44.9384 WARNING::Fitting problem for feature 132 returning NA
2025-08-21 00:02:44.980234 WARNING::Fitting problem for feature 139 returning NA
2025-08-21 00:02:45.049874 WARNING::Fitting problem for feature 150 returning NA
2025-08-21 00:02:56.931822 WARNING::Fitting problem for feature 50 returning NA
2025-08-21 00:02:57.01224 WARNING::Fitting problem for feature 62 returning NA
2025-08-21 00:02:57.090774 WARNING::Fitting problem for feature 74 returning NA
2025-08-21 00:02:57.113954 WARNING::Fitting problem for feature 78 returning NA
2025-08-21 00:02:57.148656 WARNING::Fitting problem for feature 84 returning NA
2025-08-21 00:02:57.224502 WARNING::Fitting problem for feature 96 returning NA
2025-08-21 00:02:57.229879 WARNING::Fitting problem for feature 97 returning NA
2025-08-21 00:02:57.241662 WARNING::Fitting problem for feature 99 returning NA
2025-08-21 00:02:57.338153 WARNING::Fitting problem for feature 114 returning NA
2025-08-21 00:02:57.343687 WARNING::Fitting problem for feature 115 returning NA
2025-08-21 00:02:57.394006 WARNING::Fitting problem for feature 123 returning NA
2025-08-21 00:02:57.434854 WARNING::Fitting problem for feature 130 returning NA
2025-08-21 00:02:57.447407 WARNING::Fitting problem for feature 132 returning NA
2025-08-21 00:02:57.490029 WARNING::Fitting problem for feature 139 returning NA
2025-08-21 00:02:57.563994 WARNING::Fitting problem for feature 150 returning NA
2025-08-21 00:02:57.86167 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_linear.rds
2025-08-21 00:02:57.922375 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_linear.rds
2025-08-21 00:02:57.985532 WARNING::Deleting existing residuals file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/residuals_logistic.rds
2025-08-21 00:02:58.284298 WARNING::Deleting existing fitted file: /tmp/RtmpkHO8LQ/file3f41833fd21ce3/fits/fitted_logistic.rds
2025-08-21 00:03:14.167752 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-08-21 00:03:14.185401 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-08-21 00:03:14.197734 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-08-21 00:03:14.251091 ERROR::No fixed, group, or
                        ordered effects included in formula.
2025-08-21 00:03:14.267403 ERROR::Effect name not found in metadata: d
2025-08-21 00:03:14.279145 ERROR::No user formula provided
2025-08-21 00:03:14.308786 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-08-21 00:03:14.320694 ERROR::No fixed/group/ordered/
                        feature-specific effects provided.
2025-08-21 00:03:17.197488 INFO::Writing function arguments to log file
2025-08-21 00:03:17.212053 INFO::Verifying options selected are valid
2025-08-21 00:03:19.035642 INFO::Writing function arguments to log file
2025-08-21 00:03:19.047336 INFO::Verifying options selected are valid
2025-08-21 00:03:19.048517 INFO::Determining format of input files
2025-08-21 00:03:19.049541 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-21 00:03:19.051904 INFO::Running selected normalization method: TSS
2025-08-21 00:03:19.053443 INFO::Creating output feature tables folder
2025-08-21 00:03:19.054447 INFO::Writing normalized data to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/features/data_norm.tsv
2025-08-21 00:03:19.055988 INFO::Filter data based on min abundance and min prevalence
2025-08-21 00:03:19.056932 INFO::Total samples in data: 16
2025-08-21 00:03:19.057813 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-08-21 00:03:19.059688 INFO::Total filtered features: 0
2025-08-21 00:03:19.060647 INFO::Filtered feature names from abundance and prevalence filtering:
2025-08-21 00:03:19.061806 INFO::Total features filtered by non-zero variance filtering: 0
2025-08-21 00:03:19.062753 INFO::Filtered feature names from variance filtering:
2025-08-21 00:03:19.063669 INFO::Writing filtered data to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/features/filtered_data.tsv
2025-08-21 00:03:19.06517 INFO::Running selected transform method: LOG
2025-08-21 00:03:19.066403 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/features/data_transformed.tsv
2025-08-21 00:03:19.068046 INFO::Applying z-score to standardize continuous metadata
2025-08-21 00:03:19.073541 INFO::Running the linear model component
2025-08-21 00:03:19.087491 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:19.0921 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:19.096397 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:19.103715 INFO::Counting total values for each feature
2025-08-21 00:03:19.105529 INFO::Running the logistic model component
2025-08-21 00:03:19.119879 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:19.126719 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:19.132851 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:19.141821 INFO::Counting total values for each feature
2025-08-21 00:03:19.143962 INFO::Re-running abundances for warn_prevalence
2025-08-21 00:03:19.144912 INFO::Running selected normalization method: TSS
2025-08-21 00:03:19.146392 INFO::Running selected transform method: LOG
2025-08-21 00:03:19.160271 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:19.164683 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:19.168901 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:19.25456 INFO::Creating fits folder
2025-08-21 00:03:19.255836 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/residuals_linear.rds
2025-08-21 00:03:19.257004 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/fitted_linear.rds
2025-08-21 00:03:19.258263 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/residuals_logistic.rds
2025-08-21 00:03:19.259531 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41833e3774a3/fits/fitted_logistic.rds
2025-08-21 00:03:19.262262 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpkHO8LQ/file3f41833e3774a3/all_results.tsv
2025-08-21 00:03:19.263902 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/RtmpkHO8LQ/file3f41833e3774a3/significant_results.tsv
2025-08-21 00:03:19.265281 INFO::Creating output figures folder
2025-08-21 00:03:19.266679 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures/summary_plot.pdf
2025-08-21 00:03:20.522023 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures
2025-08-21 00:03:20.52404 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-21 00:03:20.529099 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-21 00:03:20.91683 INFO::Writing summary plot of
                        significant results to file: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures/summary_plot.pdf
2025-08-21 00:03:22.185938 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpkHO8LQ/file3f41833e3774a3/figures
2025-08-21 00:03:22.187543 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-21 00:03:22.192435 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-21 00:03:22.582797 INFO::Running the linear model component
2025-08-21 00:03:22.591504 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:22.595841 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:22.599928 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:22.606869 INFO::Counting total values for each feature
2025-08-21 00:03:22.608562 INFO::Running the logistic model component
2025-08-21 00:03:22.616975 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:22.623272 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:22.629353 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:22.638304 INFO::Counting total values for each feature
2025-08-21 00:03:22.640371 INFO::Re-running abundances for warn_prevalence
2025-08-21 00:03:22.641191 INFO::Running selected normalization method: TSS
2025-08-21 00:03:22.642548 INFO::Running selected transform method: LOG
2025-08-21 00:03:22.651158 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:22.655365 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:22.659344 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:22.749075 INFO::Creating output folder
2025-08-21 00:03:22.750175 INFO::Creating output figures folder
2025-08-21 00:03:22.751499 INFO::Writing summary plot of significant
                        results to file: /tmp/RtmpkHO8LQ/file3f41833ef20514/figures/summary_plot.pdf
2025-08-21 00:03:24.046105 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpkHO8LQ/file3f41833ef20514/figures
2025-08-21 00:03:24.048162 INFO::Plotting associations from most to least significant, grouped by metadata
2025-08-21 00:03:24.054169 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-08-21 00:03:24.912592 INFO::Applying z-score to standardize continuous metadata
2025-08-21 00:03:24.920766 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-08-21 00:03:24.921747 INFO::Bypass z-score application to metadata
2025-08-21 00:03:24.92437 INFO::Bypass z-score application to metadata
2025-08-21 00:03:24.943253 INFO::Determining format of input files
2025-08-21 00:03:24.944378 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-21 00:03:24.945313 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-08-21 00:03:24.952473 INFO::Determining format of input files
2025-08-21 00:03:24.953605 INFO::Input format is data samples as columns and metadata samples as rows
2025-08-21 00:03:24.954993 INFO::Input format is feature_specific_covariate samples as columns
2025-08-21 00:03:24.962923 INFO::Determining format of input files
2025-08-21 00:03:24.963925 INFO::Input format is data samples as rows and metadata samples as rows
2025-08-21 00:03:24.964983 INFO::Input format is feature_specific_covariate samples as columns
2025-08-21 00:03:24.966656 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-08-21 00:03:24.967475 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-08-21 00:03:24.978252 INFO::Running selected transform method: LOG
2025-08-21 00:03:24.979325 INFO::Creating output feature tables folder
2025-08-21 00:03:24.980183 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv
2025-08-21 00:03:24.98372 INFO::Running selected transform method: LOG
2025-08-21 00:03:24.984688 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv
2025-08-21 00:03:24.987987 INFO::Running selected transform method: PLOG
2025-08-21 00:03:24.989446 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv
2025-08-21 00:03:24.992008 INFO::Running selected transform method: NONE
2025-08-21 00:03:24.992751 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpkHO8LQ/file3f418314b3e9a1/features/data_transformed.tsv
2025-08-21 00:03:24.999424 INFO::Running the linear model component
2025-08-21 00:03:25.00782 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:25.011981 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:25.015814 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:25.022562 INFO::Counting total values for each feature
2025-08-21 00:03:25.024152 INFO::Running the logistic model component
2025-08-21 00:03:25.032341 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:25.038427 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:25.04413 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:25.052557 INFO::Counting total values for each feature
2025-08-21 00:03:25.054488 INFO::Re-running abundances for warn_prevalence
2025-08-21 00:03:25.055278 INFO::Running selected normalization method: TSS
2025-08-21 00:03:25.056617 INFO::Running selected transform method: LOG
2025-08-21 00:03:25.064958 INFO::Fitting model to feature number 1, a
2025-08-21 00:03:25.069044 INFO::Fitting model to feature number 2, b
2025-08-21 00:03:25.072941 INFO::Fitting model to feature number 3, c
2025-08-21 00:03:25.157548 INFO::Creating output folder
2025-08-21 00:03:25.15853 INFO::Creating fits folder
2025-08-21 00:03:25.159384 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/residuals_linear.rds
2025-08-21 00:03:25.160372 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/fitted_linear.rds
2025-08-21 00:03:25.16144 INFO::Writing residuals to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/residuals_logistic.rds
2025-08-21 00:03:25.162476 INFO::Writing fitted values to file /tmp/RtmpkHO8LQ/file3f41837f0da59f/fits/fitted_logistic.rds
2025-08-21 00:03:25.164972 INFO::Writing all the results to file (ordered 
            by increasing individual q-values): /tmp/RtmpkHO8LQ/file3f41837f0da59f/all_results.tsv
2025-08-21 00:03:25.166439 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/RtmpkHO8LQ/file3f41837f0da59f/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
> 
> 
> proc.time()
   user  system elapsed 
307.936   4.453 312.384 

Example timings

maaslin3.Rcheck/maaslin3-Ex.timings

nameusersystemelapsed
maaslin319.035 0.62619.666
maaslin_check_arguments0.1380.0020.139
maaslin_check_formula0.1300.0050.137
maaslin_compute_formula0.1330.0040.139
maaslin_contrast_test19.193 0.63219.827
maaslin_filter0.4390.0230.462
maaslin_fit13.434 0.08913.524
maaslin_log_arguments0.1300.0030.133
maaslin_normalize0.2870.0100.297
maaslin_plot_results36.438 0.52736.928
maaslin_plot_results_from_output35.478 0.34135.821
maaslin_process_metadata0.4380.0200.458
maaslin_read_data0.1320.0050.137
maaslin_reorder_data0.1380.0040.142
maaslin_transform0.5770.0120.588
maaslin_write_results13.440 0.28213.722
maaslin_write_results_lefse_format14.989 0.09415.084
preprocess_dna_mtx0.0030.0000.004
preprocess_taxa_mtx0.0040.0000.004