William Nickols
| Snapshot Date: 2025-11-02 13:45 -0500 (Sun, 02 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-03 12:05 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 1170/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.2.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: maaslin3 |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-11-02 20:29:13 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 20:34:05 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 291.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 16.690 0.709 17.543
maaslin_plot_results 16.102 0.688 16.851
maaslin3 8.637 0.524 9.708
maaslin_contrast_test 7.208 0.660 8.179
maaslin_write_results 5.862 0.504 6.375
maaslin_fit 5.303 0.607 5.928
maaslin_write_results_lefse_format 5.425 0.433 5.868
* 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
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 ‘1.2.0’ ** 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)
maaslin3.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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")
2025-11-02 20:31:42.423745 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:31:42.722921 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:31:42.747928 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:31:42.755294 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:31:42.767197 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:31:42.797019 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:31:42.798873 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:31:42.802705 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:31:42.83392 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:31:42.835824 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:31:42.851911 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:31:42.864605 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:31:42.872357 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:31:42.885191 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:31:42.907536 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:31:49.451645 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:31:49.479483 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:31:49.505838 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:31:49.513466 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:31:49.525345 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:31:49.552089 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:31:49.554196 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:31:49.558578 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:31:49.605573 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:31:49.607622 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:31:49.624573 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:31:49.638678 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:31:49.643041 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:31:49.657183 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:31:49.685662 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:31:51.099 R[42106:611826461] XType: Using static font registry.
2025-11-02 20:31:58.719803 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:31:58.747166 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:31:58.774977 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:31:58.782839 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:31:58.795078 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:31:58.821324 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:31:58.823464 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:31:58.8278 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:31:59.270331 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:31:59.272461 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:31:59.28977 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:31:59.304096 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:31:59.308509 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:31:59.323119 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:31:59.347756 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:04.617114 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:04.642781 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:04.667921 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:04.6754 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:04.687407 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:04.7138 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:04.715994 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:04.720228 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:04.752795 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:04.754815 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:04.772146 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:04.785535 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:04.789847 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:04.803635 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:04.827194 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:04.909985 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/residuals_linear.rds
2025-11-02 20:32:04.945844 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/fitted_linear.rds
2025-11-02 20:32:04.979302 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/residuals_logistic.rds
2025-11-02 20:32:05.146753 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/fitted_logistic.rds
2025-11-02 20:32:13.277152 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:13.304581 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:13.33836 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:13.346167 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:13.3581 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:13.384384 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:13.386422 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:13.390593 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:13.423817 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:13.425945 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:13.442928 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:13.457044 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:13.461556 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:13.475963 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:13.500983 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:19.466578 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:19.493679 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:19.521833 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:19.53002 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:19.542697 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:19.57266 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:19.574959 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:19.579657 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:19.641244 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:19.643303 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:19.660062 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:19.673418 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:19.677535 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:19.691183 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:19.71394 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:19.782311 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/residuals_linear.rds
2025-11-02 20:32:19.814557 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/fitted_linear.rds
2025-11-02 20:32:19.84802 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/residuals_logistic.rds
2025-11-02 20:32:20.016805 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/fitted_logistic.rds
2025-11-02 20:32:28.159938 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:28.186526 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:28.213404 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:28.221464 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:28.234001 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:28.262117 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:28.264248 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:28.283918 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:28.317398 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:28.319516 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:28.337064 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:28.351729 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:28.35629 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:28.370764 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:28.3959 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:33.418382 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:33.445195 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:33.471096 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:33.478952 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:33.491064 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:33.518487 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:33.520571 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:33.524821 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:33.564308 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:33.566565 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:33.583679 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:33.597667 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:33.601926 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:33.615932 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:33.640147 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:33.719916 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/residuals_linear.rds
2025-11-02 20:32:33.753038 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/fitted_linear.rds
2025-11-02 20:32:33.787127 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/residuals_logistic.rds
2025-11-02 20:32:33.95817 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a52c34538/fits/fitted_logistic.rds
2025-11-02 20:32:42.09218 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:42.119067 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:42.145103 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:42.152849 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:42.164954 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:42.198364 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:42.200524 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:42.204813 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:42.239754 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:42.241866 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:42.260802 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:42.276894 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:42.281289 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:42.295702 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:42.323267 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:47.525674 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:32:47.5523 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:32:47.578534 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:32:47.586241 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:32:47.598247 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:32:47.624635 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:32:47.62669 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:32:47.630958 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:32:47.664358 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:32:47.666431 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:32:47.683802 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:32:47.698142 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:32:47.702654 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:32:47.716661 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:32:47.740401 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:32:56.778306 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:00.790019 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:10.077834 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:13.893349 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:14.080984 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_linear.rds
2025-11-02 20:33:14.114196 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_linear.rds
2025-11-02 20:33:14.137043 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_logistic.rds
2025-11-02 20:33:14.178438 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_logistic.rds
2025-11-02 20:33:23.02152 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:25.758672 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:25.855949 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_linear.rds
2025-11-02 20:33:25.888544 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_linear.rds
2025-11-02 20:33:25.911222 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_logistic.rds
2025-11-02 20:33:25.951502 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_logistic.rds
2025-11-02 20:33:33.256338 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:35.893899 WARNING::Fitting problem for feature 124 returning NA
2025-11-02 20:33:35.99284 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_linear.rds
2025-11-02 20:33:36.025709 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_linear.rds
2025-11-02 20:33:36.048323 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_logistic.rds
2025-11-02 20:33:36.088171 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_logistic.rds
2025-11-02 20:33:43.207911 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:33:43.234921 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:33:43.261447 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:33:43.269583 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:33:43.282239 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:33:43.309764 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:33:43.311916 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:33:43.31596 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:33:43.348977 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:33:43.351046 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:33:43.386098 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:33:43.399718 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:33:43.403922 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:33:43.417612 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:33:43.441781 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:33:48.589003 WARNING::Fitting problem for feature 50 returning NA
2025-11-02 20:33:48.638592 WARNING::Fitting problem for feature 62 returning NA
2025-11-02 20:33:48.663674 WARNING::Fitting problem for feature 74 returning NA
2025-11-02 20:33:48.671175 WARNING::Fitting problem for feature 78 returning NA
2025-11-02 20:33:48.682757 WARNING::Fitting problem for feature 84 returning NA
2025-11-02 20:33:48.708429 WARNING::Fitting problem for feature 96 returning NA
2025-11-02 20:33:48.710381 WARNING::Fitting problem for feature 97 returning NA
2025-11-02 20:33:48.71435 WARNING::Fitting problem for feature 99 returning NA
2025-11-02 20:33:48.747125 WARNING::Fitting problem for feature 114 returning NA
2025-11-02 20:33:48.749248 WARNING::Fitting problem for feature 115 returning NA
2025-11-02 20:33:48.766856 WARNING::Fitting problem for feature 123 returning NA
2025-11-02 20:33:48.780671 WARNING::Fitting problem for feature 130 returning NA
2025-11-02 20:33:48.785001 WARNING::Fitting problem for feature 132 returning NA
2025-11-02 20:33:48.798625 WARNING::Fitting problem for feature 139 returning NA
2025-11-02 20:33:48.821351 WARNING::Fitting problem for feature 150 returning NA
2025-11-02 20:33:48.905121 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_linear.rds
2025-11-02 20:33:48.937572 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_linear.rds
2025-11-02 20:33:48.971025 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/residuals_logistic.rds
2025-11-02 20:33:49.138182 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5324367b/fits/fitted_logistic.rds
2025-11-02 20:33:56.775843 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-02 20:33:56.781537 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-02 20:33:56.785235 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-02 20:33:56.807133 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-02 20:33:56.812524 ERROR::Effect name not found in metadata: d
2025-11-02 20:33:56.816068 ERROR::No user formula provided
2025-11-02 20:33:56.825531 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-02 20:33:56.829321 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-02 20:33:57.921182 INFO::Writing function arguments to log file
2025-11-02 20:33:57.926414 INFO::Verifying options selected are valid
2025-11-02 20:33:58.77888 INFO::Writing function arguments to log file
2025-11-02 20:33:58.783154 INFO::Verifying options selected are valid
2025-11-02 20:33:58.783507 INFO::Determining format of input files
2025-11-02 20:33:58.783794 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-02 20:33:58.784541 INFO::Running selected normalization method: TSS
2025-11-02 20:33:58.785053 INFO::Creating output feature tables folder
2025-11-02 20:33:58.785417 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/features/data_norm.tsv
2025-11-02 20:33:58.785949 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-02 20:33:58.786227 INFO::Total samples in data: 16
2025-11-02 20:33:58.786494 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-02 20:33:58.786752 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-02 20:33:58.787352 INFO::Total filtered features: 0
2025-11-02 20:33:58.787664 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-02 20:33:58.788022 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-02 20:33:58.788306 INFO::Filtered feature names from variance filtering:
2025-11-02 20:33:58.788575 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/features/filtered_data.tsv
2025-11-02 20:33:58.789075 INFO::Running selected transform method: LOG
2025-11-02 20:33:58.789453 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/features/data_transformed.tsv
2025-11-02 20:33:58.790016 INFO::Applying z-score to standardize continuous metadata
2025-11-02 20:33:58.791795 INFO::Running the linear model component
2025-11-02 20:33:58.796486 INFO::Fitting model to feature number 1, a
2025-11-02 20:33:58.797965 INFO::Fitting model to feature number 2, b
2025-11-02 20:33:58.799276 INFO::Fitting model to feature number 3, c
2025-11-02 20:33:58.801581 INFO::Counting total values for each feature
2025-11-02 20:33:58.802224 INFO::Running the logistic model component
2025-11-02 20:33:58.806948 INFO::Fitting model to feature number 1, a
2025-11-02 20:33:58.80902 INFO::Fitting model to feature number 2, b
2025-11-02 20:33:58.810878 INFO::Fitting model to feature number 3, c
2025-11-02 20:33:58.813745 INFO::Counting total values for each feature
2025-11-02 20:33:58.814509 INFO::Re-running abundances for warn_prevalence
2025-11-02 20:33:58.814876 INFO::Running selected normalization method: TSS
2025-11-02 20:33:58.815385 INFO::Running selected transform method: LOG
2025-11-02 20:33:58.820211 INFO::Fitting model to feature number 1, a
2025-11-02 20:33:58.821626 INFO::Fitting model to feature number 2, b
2025-11-02 20:33:58.822904 INFO::Fitting model to feature number 3, c
2025-11-02 20:33:58.849289 INFO::Creating fits folder
2025-11-02 20:33:58.849863 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/fits/residuals_linear.rds
2025-11-02 20:33:58.85047 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/fits/fitted_linear.rds
2025-11-02 20:33:58.851048 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/fits/residuals_logistic.rds
2025-11-02 20:33:58.851534 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/fits/fitted_logistic.rds
2025-11-02 20:33:58.852535 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/all_results.tsv
2025-11-02 20:33:58.853197 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//Rtmp7TuwtW/filea47a29b6213e/significant_results.tsv
2025-11-02 20:33:58.853693 INFO::Creating output figures folder
2025-11-02 20:33:58.854172 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/figures/summary_plot.pdf
2025-11-02 20:33:59.435144 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/figures
2025-11-02 20:33:59.436105 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-02 20:33:59.438299 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-02 20:33:59.648494 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/figures/summary_plot.pdf
2025-11-02 20:34:00.237142 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a29b6213e/figures
2025-11-02 20:34:00.237743 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-02 20:34:00.239651 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-02 20:34:00.436042 INFO::Running the linear model component
2025-11-02 20:34:00.438953 INFO::Fitting model to feature number 1, a
2025-11-02 20:34:00.440489 INFO::Fitting model to feature number 2, b
2025-11-02 20:34:00.441733 INFO::Fitting model to feature number 3, c
2025-11-02 20:34:00.444148 INFO::Counting total values for each feature
2025-11-02 20:34:00.444713 INFO::Running the logistic model component
2025-11-02 20:34:00.447317 INFO::Fitting model to feature number 1, a
2025-11-02 20:34:00.449354 INFO::Fitting model to feature number 2, b
2025-11-02 20:34:00.451168 INFO::Fitting model to feature number 3, c
2025-11-02 20:34:00.454049 INFO::Counting total values for each feature
2025-11-02 20:34:00.454728 INFO::Re-running abundances for warn_prevalence
2025-11-02 20:34:00.454967 INFO::Running selected normalization method: TSS
2025-11-02 20:34:00.455413 INFO::Running selected transform method: LOG
2025-11-02 20:34:00.458088 INFO::Fitting model to feature number 1, a
2025-11-02 20:34:00.459412 INFO::Fitting model to feature number 2, b
2025-11-02 20:34:00.460614 INFO::Fitting model to feature number 3, c
2025-11-02 20:34:00.489173 INFO::Creating output folder
2025-11-02 20:34:00.489626 INFO::Creating output figures folder
2025-11-02 20:34:00.490101 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5c8e4933/figures/summary_plot.pdf
2025-11-02 20:34:01.08998 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5c8e4933/figures
2025-11-02 20:34:01.090568 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-02 20:34:01.092349 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-02 20:34:01.474885 INFO::Applying z-score to standardize continuous metadata
2025-11-02 20:34:01.477508 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-02 20:34:01.477785 INFO::Bypass z-score application to metadata
2025-11-02 20:34:01.478527 INFO::Bypass z-score application to metadata
2025-11-02 20:34:01.48486 INFO::Determining format of input files
2025-11-02 20:34:01.485165 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-02 20:34:01.485411 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-02 20:34:01.487502 INFO::Determining format of input files
2025-11-02 20:34:01.48782 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-02 20:34:01.488194 INFO::Input format is feature_specific_covariate samples as columns
2025-11-02 20:34:01.490515 INFO::Determining format of input files
2025-11-02 20:34:01.490794 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-02 20:34:01.49109 INFO::Input format is feature_specific_covariate samples as columns
2025-11-02 20:34:01.49154 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-02 20:34:01.491753 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-02 20:34:01.495188 INFO::Running selected transform method: LOG
2025-11-02 20:34:01.495524 INFO::Creating output feature tables folder
2025-11-02 20:34:01.49589 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a472ed78a/features/data_transformed.tsv
2025-11-02 20:34:01.497152 INFO::Running selected transform method: LOG
2025-11-02 20:34:01.497465 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a472ed78a/features/data_transformed.tsv
2025-11-02 20:34:01.498627 INFO::Running selected transform method: PLOG
2025-11-02 20:34:01.499103 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a472ed78a/features/data_transformed.tsv
2025-11-02 20:34:01.499967 INFO::Running selected transform method: NONE
2025-11-02 20:34:01.500203 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a472ed78a/features/data_transformed.tsv
2025-11-02 20:34:01.502768 INFO::Running the linear model component
2025-11-02 20:34:01.505361 INFO::Fitting model to feature number 1, a
2025-11-02 20:34:01.506737 INFO::Fitting model to feature number 2, b
2025-11-02 20:34:01.507927 INFO::Fitting model to feature number 3, c
2025-11-02 20:34:01.510161 INFO::Counting total values for each feature
2025-11-02 20:34:01.510694 INFO::Running the logistic model component
2025-11-02 20:34:01.513216 INFO::Fitting model to feature number 1, a
2025-11-02 20:34:01.51512 INFO::Fitting model to feature number 2, b
2025-11-02 20:34:01.516864 INFO::Fitting model to feature number 3, c
2025-11-02 20:34:01.519559 INFO::Counting total values for each feature
2025-11-02 20:34:01.520201 INFO::Re-running abundances for warn_prevalence
2025-11-02 20:34:01.520439 INFO::Running selected normalization method: TSS
2025-11-02 20:34:01.520854 INFO::Running selected transform method: LOG
2025-11-02 20:34:01.523423 INFO::Fitting model to feature number 1, a
2025-11-02 20:34:01.524655 INFO::Fitting model to feature number 2, b
2025-11-02 20:34:01.525801 INFO::Fitting model to feature number 3, c
2025-11-02 20:34:01.55191 INFO::Creating output folder
2025-11-02 20:34:01.552333 INFO::Creating fits folder
2025-11-02 20:34:01.552651 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5448c988/fits/residuals_linear.rds
2025-11-02 20:34:01.553083 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5448c988/fits/fitted_linear.rds
2025-11-02 20:34:01.553439 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5448c988/fits/residuals_logistic.rds
2025-11-02 20:34:01.553803 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5448c988/fits/fitted_logistic.rds
2025-11-02 20:34:01.55465 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp7TuwtW/filea47a5448c988/all_results.tsv
2025-11-02 20:34:01.555227 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//Rtmp7TuwtW/filea47a5448c988/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
137.072 5.577 143.391
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.637 | 0.524 | 9.708 | |
| maaslin_check_arguments | 0.061 | 0.001 | 0.067 | |
| maaslin_check_formula | 0.060 | 0.003 | 0.064 | |
| maaslin_compute_formula | 0.069 | 0.005 | 0.088 | |
| maaslin_contrast_test | 7.208 | 0.660 | 8.179 | |
| maaslin_filter | 0.220 | 0.031 | 0.253 | |
| maaslin_fit | 5.303 | 0.607 | 5.928 | |
| maaslin_log_arguments | 0.055 | 0.004 | 0.059 | |
| maaslin_normalize | 0.137 | 0.019 | 0.157 | |
| maaslin_plot_results | 16.102 | 0.688 | 16.851 | |
| maaslin_plot_results_from_output | 16.690 | 0.709 | 17.543 | |
| maaslin_process_metadata | 0.222 | 0.015 | 0.245 | |
| maaslin_read_data | 0.054 | 0.002 | 0.057 | |
| maaslin_reorder_data | 0.053 | 0.003 | 0.057 | |
| maaslin_transform | 0.272 | 0.022 | 0.300 | |
| maaslin_write_results | 5.862 | 0.504 | 6.375 | |
| maaslin_write_results_lefse_format | 5.425 | 0.433 | 5.868 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.001 | |
| preprocess_taxa_mtx | 0.001 | 0.001 | 0.002 | |