William Nickols
| Snapshot Date: 2025-11-03 13:45 -0500 (Mon, 03 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 2025-11-04 12:04 -0500 (Tue, 04 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: 2025-11-03 22:12:13 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 22:26:03 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 830.3 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: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.2.0’
* 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 49.802 1.005 51.150
maaslin_plot_results_from_output 49.414 1.083 50.921
maaslin3 22.284 1.077 23.681
maaslin_contrast_test 20.669 1.206 22.098
maaslin_write_results_lefse_format 18.230 0.868 19.229
maaslin_write_results 15.532 0.532 16.179
maaslin_fit 13.732 0.930 14.767
* 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-x86_64/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: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-11-03 22:19:12.795628 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:19:13.565252 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:19:13.673192 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:19:13.702759 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:19:13.746917 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:19:13.852274 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:19:13.857785 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:19:13.874463 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:19:13.98177 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:19:13.988308 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:19:14.047224 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:19:14.099322 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:19:14.12445 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:19:14.175332 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:19:14.268365 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:19:31.829547 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:19:31.923118 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:19:32.025666 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:19:32.055989 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:19:32.098613 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:19:32.189277 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:19:32.194478 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:19:32.21245 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:19:32.364783 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:19:32.372566 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:19:32.428967 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:19:32.478069 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:19:32.491167 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:19:32.547052 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:19:32.619585 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:19:37.129 R[72100:725058543] XType: com.apple.fonts is not accessible.
2025-11-03 22:19:37.129 R[72100:725058543] XType: XTFontStaticRegistry is enabled.
2025-11-03 22:19:59.104393 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:19:59.209898 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:19:59.30952 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:19:59.340161 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:19:59.379294 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:19:59.475815 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:19:59.484471 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:19:59.497665 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:20:00.50675 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:20:00.514631 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:20:00.575423 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:20:00.621779 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:20:00.635268 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:20:00.688071 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:20:00.78569 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:20:15.886946 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:20:15.990208 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:20:16.085506 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:20:16.113243 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:20:16.162857 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:20:16.259352 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:20:16.265872 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:20:16.279354 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:20:16.386815 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:20:16.393049 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:20:16.44802 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:20:16.497169 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:20:16.511977 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:20:16.560849 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:20:16.637732 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:20:16.885774 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/residuals_linear.rds
2025-11-03 22:20:16.957475 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/fitted_linear.rds
2025-11-03 22:20:17.027221 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/residuals_logistic.rds
2025-11-03 22:20:17.380245 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/fitted_logistic.rds
2025-11-03 22:20:42.14955 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:20:42.253991 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:20:42.340428 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:20:42.36982 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:20:42.417592 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:20:42.518477 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:20:42.525294 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:20:42.543529 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:20:42.657744 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:20:42.663773 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:20:42.72729 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:20:42.783688 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:20:42.80252 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:20:42.852332 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:20:42.944699 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:20:58.869722 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:20:58.968015 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:20:59.070284 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:20:59.09556 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:20:59.133796 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:20:59.238644 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:20:59.245709 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:20:59.260346 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:20:59.426391 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:20:59.433167 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:20:59.498971 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:20:59.543316 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:20:59.556759 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:20:59.59978 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:20:59.680166 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:20:59.908994 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/residuals_linear.rds
2025-11-03 22:20:59.976421 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/fitted_linear.rds
2025-11-03 22:21:00.050307 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/residuals_logistic.rds
2025-11-03 22:21:00.4046 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/fitted_logistic.rds
2025-11-03 22:21:24.296595 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:21:24.400485 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:21:24.500363 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:21:24.530337 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:21:24.572228 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:21:24.676384 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:21:24.684331 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:21:24.738031 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:21:24.859978 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:21:24.866273 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:21:24.936052 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:21:24.987736 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:21:25.003 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:21:25.055879 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:21:25.146009 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:21:39.172455 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:21:39.278924 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:21:39.388133 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:21:39.423258 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:21:39.474733 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:21:39.584715 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:21:39.595688 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:21:39.616626 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:21:39.751466 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:21:39.75721 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:21:39.819923 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:21:39.869768 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:21:39.885409 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:21:39.93121 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:21:40.009977 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:21:40.250126 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/residuals_linear.rds
2025-11-03 22:21:40.313188 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/fitted_linear.rds
2025-11-03 22:21:40.378681 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/residuals_logistic.rds
2025-11-03 22:21:40.728251 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a4498025fd/fits/fitted_logistic.rds
2025-11-03 22:22:05.348747 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:22:05.454497 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:22:05.555792 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:22:05.583593 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:22:05.628311 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:22:05.727146 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:22:05.734055 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:22:05.747234 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:22:05.861724 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:22:05.867686 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:22:05.933864 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:22:05.9801 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:22:05.996818 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:22:06.047452 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:22:06.119684 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:22:19.320557 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:22:19.418805 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:22:19.511498 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:22:19.541642 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:22:19.585191 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:22:19.688915 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:22:19.695767 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:22:19.71274 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:22:19.844878 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:22:19.853047 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:22:19.922389 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:22:19.971406 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:22:19.988939 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:22:20.041218 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:22:20.161868 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:22:47.150751 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:22:57.931318 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:23:25.170762 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:23:35.946144 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:23:36.649531 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_linear.rds
2025-11-03 22:23:36.714456 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_linear.rds
2025-11-03 22:23:36.754727 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_logistic.rds
2025-11-03 22:23:36.823445 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_logistic.rds
2025-11-03 22:24:02.378842 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:24:09.367917 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:24:09.743865 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_linear.rds
2025-11-03 22:24:09.821005 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_linear.rds
2025-11-03 22:24:09.865265 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_logistic.rds
2025-11-03 22:24:09.945703 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_logistic.rds
2025-11-03 22:24:31.512383 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:24:38.865088 WARNING::Fitting problem for feature 124 returning NA
2025-11-03 22:24:39.236591 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_linear.rds
2025-11-03 22:24:39.302167 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_linear.rds
2025-11-03 22:24:39.33648 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_logistic.rds
2025-11-03 22:24:39.410105 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_logistic.rds
2025-11-03 22:24:59.583861 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:24:59.673979 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:24:59.768852 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:24:59.793736 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:24:59.82882 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:24:59.920905 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:24:59.92695 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:24:59.942242 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:25:00.052149 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:25:00.061142 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:25:00.155359 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:25:00.197251 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:25:00.211426 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:25:00.256509 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:25:00.335193 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:25:13.550964 WARNING::Fitting problem for feature 50 returning NA
2025-11-03 22:25:13.684387 WARNING::Fitting problem for feature 62 returning NA
2025-11-03 22:25:13.77191 WARNING::Fitting problem for feature 74 returning NA
2025-11-03 22:25:13.79624 WARNING::Fitting problem for feature 78 returning NA
2025-11-03 22:25:13.835742 WARNING::Fitting problem for feature 84 returning NA
2025-11-03 22:25:13.923159 WARNING::Fitting problem for feature 96 returning NA
2025-11-03 22:25:13.928484 WARNING::Fitting problem for feature 97 returning NA
2025-11-03 22:25:13.941214 WARNING::Fitting problem for feature 99 returning NA
2025-11-03 22:25:14.049339 WARNING::Fitting problem for feature 114 returning NA
2025-11-03 22:25:14.057471 WARNING::Fitting problem for feature 115 returning NA
2025-11-03 22:25:14.120014 WARNING::Fitting problem for feature 123 returning NA
2025-11-03 22:25:14.174481 WARNING::Fitting problem for feature 130 returning NA
2025-11-03 22:25:14.189719 WARNING::Fitting problem for feature 132 returning NA
2025-11-03 22:25:14.234477 WARNING::Fitting problem for feature 139 returning NA
2025-11-03 22:25:14.315192 WARNING::Fitting problem for feature 150 returning NA
2025-11-03 22:25:14.613246 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_linear.rds
2025-11-03 22:25:14.68198 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_linear.rds
2025-11-03 22:25:14.745912 WARNING::Deleting existing residuals file: /tmp/RtmpgNfaQa/file119a448989647/fits/residuals_logistic.rds
2025-11-03 22:25:15.095197 WARNING::Deleting existing fitted file: /tmp/RtmpgNfaQa/file119a448989647/fits/fitted_logistic.rds
2025-11-03 22:25:38.142604 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-03 22:25:38.163556 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-03 22:25:38.176775 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-03 22:25:38.256701 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-03 22:25:38.274082 ERROR::Effect name not found in metadata: d
2025-11-03 22:25:38.291605 ERROR::No user formula provided
2025-11-03 22:25:38.327079 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-03 22:25:38.345184 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-03 22:25:41.864785 INFO::Writing function arguments to log file
2025-11-03 22:25:41.885943 INFO::Verifying options selected are valid
2025-11-03 22:25:44.487299 INFO::Writing function arguments to log file
2025-11-03 22:25:44.506867 INFO::Verifying options selected are valid
2025-11-03 22:25:44.508048 INFO::Determining format of input files
2025-11-03 22:25:44.509146 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-03 22:25:44.511774 INFO::Running selected normalization method: TSS
2025-11-03 22:25:44.513749 INFO::Creating output feature tables folder
2025-11-03 22:25:44.515587 INFO::Writing normalized data to file /tmp/RtmpgNfaQa/file119a4343bcf08/features/data_norm.tsv
2025-11-03 22:25:44.518049 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-03 22:25:44.519056 INFO::Total samples in data: 16
2025-11-03 22:25:44.520014 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-03 22:25:44.52121 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-03 22:25:44.524136 INFO::Total filtered features: 0
2025-11-03 22:25:44.525842 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-03 22:25:44.527561 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-03 22:25:44.528657 INFO::Filtered feature names from variance filtering:
2025-11-03 22:25:44.529641 INFO::Writing filtered data to file /tmp/RtmpgNfaQa/file119a4343bcf08/features/filtered_data.tsv
2025-11-03 22:25:44.531494 INFO::Running selected transform method: LOG
2025-11-03 22:25:44.532779 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgNfaQa/file119a4343bcf08/features/data_transformed.tsv
2025-11-03 22:25:44.535202 INFO::Applying z-score to standardize continuous metadata
2025-11-03 22:25:44.540738 INFO::Running the linear model component
2025-11-03 22:25:44.565984 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:44.571133 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:44.576938 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:44.586217 INFO::Counting total values for each feature
2025-11-03 22:25:44.589298 INFO::Running the logistic model component
2025-11-03 22:25:44.609482 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:44.619855 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:44.626702 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:44.636454 INFO::Counting total values for each feature
2025-11-03 22:25:44.638831 INFO::Re-running abundances for warn_prevalence
2025-11-03 22:25:44.640064 INFO::Running selected normalization method: TSS
2025-11-03 22:25:44.641894 INFO::Running selected transform method: LOG
2025-11-03 22:25:44.666358 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:44.672186 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:44.678728 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:44.783624 INFO::Creating fits folder
2025-11-03 22:25:44.785184 INFO::Writing residuals to file /tmp/RtmpgNfaQa/file119a4343bcf08/fits/residuals_linear.rds
2025-11-03 22:25:44.78669 INFO::Writing fitted values to file /tmp/RtmpgNfaQa/file119a4343bcf08/fits/fitted_linear.rds
2025-11-03 22:25:44.788112 INFO::Writing residuals to file /tmp/RtmpgNfaQa/file119a4343bcf08/fits/residuals_logistic.rds
2025-11-03 22:25:44.789547 INFO::Writing fitted values to file /tmp/RtmpgNfaQa/file119a4343bcf08/fits/fitted_logistic.rds
2025-11-03 22:25:44.79255 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgNfaQa/file119a4343bcf08/all_results.tsv
2025-11-03 22:25:44.795215 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/RtmpgNfaQa/file119a4343bcf08/significant_results.tsv
2025-11-03 22:25:44.797631 INFO::Creating output figures folder
2025-11-03 22:25:44.799444 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgNfaQa/file119a4343bcf08/figures/summary_plot.pdf
2025-11-03 22:25:46.675328 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgNfaQa/file119a4343bcf08/figures
2025-11-03 22:25:46.677755 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-03 22:25:46.686202 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-03 22:25:47.279382 INFO::Writing summary plot of
significant results to file: /tmp/RtmpgNfaQa/file119a4343bcf08/figures/summary_plot.pdf
2025-11-03 22:25:49.234324 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgNfaQa/file119a4343bcf08/figures
2025-11-03 22:25:49.23647 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-03 22:25:49.24282 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-03 22:25:49.854299 INFO::Running the linear model component
2025-11-03 22:25:49.862983 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:49.867869 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:49.872105 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:49.881528 INFO::Counting total values for each feature
2025-11-03 22:25:49.88379 INFO::Running the logistic model component
2025-11-03 22:25:49.894314 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:49.903 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:49.911478 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:49.922537 INFO::Counting total values for each feature
2025-11-03 22:25:49.92474 INFO::Re-running abundances for warn_prevalence
2025-11-03 22:25:49.92556 INFO::Running selected normalization method: TSS
2025-11-03 22:25:49.926824 INFO::Running selected transform method: LOG
2025-11-03 22:25:49.938414 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:49.944498 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:49.948709 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:50.065599 INFO::Creating output folder
2025-11-03 22:25:50.066811 INFO::Creating output figures folder
2025-11-03 22:25:50.068294 INFO::Writing summary plot of significant
results to file: /tmp/RtmpgNfaQa/file119a41bfbad19/figures/summary_plot.pdf
2025-11-03 22:25:51.96721 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpgNfaQa/file119a41bfbad19/figures
2025-11-03 22:25:51.969498 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-03 22:25:51.976503 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-03 22:25:53.175396 INFO::Applying z-score to standardize continuous metadata
2025-11-03 22:25:53.183038 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-03 22:25:53.183868 INFO::Bypass z-score application to metadata
2025-11-03 22:25:53.186489 INFO::Bypass z-score application to metadata
2025-11-03 22:25:53.212185 INFO::Determining format of input files
2025-11-03 22:25:53.21373 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-03 22:25:53.215197 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-03 22:25:53.226816 INFO::Determining format of input files
2025-11-03 22:25:53.228633 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-03 22:25:53.230179 INFO::Input format is feature_specific_covariate samples as columns
2025-11-03 22:25:53.240069 INFO::Determining format of input files
2025-11-03 22:25:53.241644 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-03 22:25:53.243199 INFO::Input format is feature_specific_covariate samples as columns
2025-11-03 22:25:53.245134 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-03 22:25:53.245842 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-03 22:25:53.258365 INFO::Running selected transform method: LOG
2025-11-03 22:25:53.25954 INFO::Creating output feature tables folder
2025-11-03 22:25:53.260607 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgNfaQa/file119a42a66f9f/features/data_transformed.tsv
2025-11-03 22:25:53.265522 INFO::Running selected transform method: LOG
2025-11-03 22:25:53.267054 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgNfaQa/file119a42a66f9f/features/data_transformed.tsv
2025-11-03 22:25:53.270951 INFO::Running selected transform method: PLOG
2025-11-03 22:25:53.273137 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgNfaQa/file119a42a66f9f/features/data_transformed.tsv
2025-11-03 22:25:53.276838 INFO::Running selected transform method: NONE
2025-11-03 22:25:53.277648 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpgNfaQa/file119a42a66f9f/features/data_transformed.tsv
2025-11-03 22:25:53.28943 INFO::Running the linear model component
2025-11-03 22:25:53.302666 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:53.307351 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:53.311456 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:53.319304 INFO::Counting total values for each feature
2025-11-03 22:25:53.32099 INFO::Running the logistic model component
2025-11-03 22:25:53.331464 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:53.339018 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:53.347469 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:53.360562 INFO::Counting total values for each feature
2025-11-03 22:25:53.363775 INFO::Re-running abundances for warn_prevalence
2025-11-03 22:25:53.365063 INFO::Running selected normalization method: TSS
2025-11-03 22:25:53.367341 INFO::Running selected transform method: LOG
2025-11-03 22:25:53.378122 INFO::Fitting model to feature number 1, a
2025-11-03 22:25:53.38304 INFO::Fitting model to feature number 2, b
2025-11-03 22:25:53.386956 INFO::Fitting model to feature number 3, c
2025-11-03 22:25:53.487876 INFO::Creating output folder
2025-11-03 22:25:53.488972 INFO::Creating fits folder
2025-11-03 22:25:53.489986 INFO::Writing residuals to file /tmp/RtmpgNfaQa/file119a47cea3114/fits/residuals_linear.rds
2025-11-03 22:25:53.491104 INFO::Writing fitted values to file /tmp/RtmpgNfaQa/file119a47cea3114/fits/fitted_linear.rds
2025-11-03 22:25:53.49282 INFO::Writing residuals to file /tmp/RtmpgNfaQa/file119a47cea3114/fits/residuals_logistic.rds
2025-11-03 22:25:53.494425 INFO::Writing fitted values to file /tmp/RtmpgNfaQa/file119a47cea3114/fits/fitted_logistic.rds
2025-11-03 22:25:53.497022 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpgNfaQa/file119a47cea3114/all_results.tsv
2025-11-03 22:25:53.498607 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/RtmpgNfaQa/file119a47cea3114/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
402.312 8.052 412.969
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 22.284 | 1.077 | 23.681 | |
| maaslin_check_arguments | 0.166 | 0.004 | 0.172 | |
| maaslin_check_formula | 0.186 | 0.013 | 0.201 | |
| maaslin_compute_formula | 0.201 | 0.011 | 0.213 | |
| maaslin_contrast_test | 20.669 | 1.206 | 22.098 | |
| maaslin_filter | 0.571 | 0.043 | 0.621 | |
| maaslin_fit | 13.732 | 0.930 | 14.767 | |
| maaslin_log_arguments | 0.161 | 0.009 | 0.171 | |
| maaslin_normalize | 0.381 | 0.043 | 0.428 | |
| maaslin_plot_results | 49.802 | 1.005 | 51.150 | |
| maaslin_plot_results_from_output | 49.414 | 1.083 | 50.921 | |
| maaslin_process_metadata | 0.603 | 0.037 | 0.645 | |
| maaslin_read_data | 0.158 | 0.009 | 0.169 | |
| maaslin_reorder_data | 0.160 | 0.010 | 0.172 | |
| maaslin_transform | 0.784 | 0.074 | 0.868 | |
| maaslin_write_results | 15.532 | 0.532 | 16.179 | |
| maaslin_write_results_lefse_format | 18.230 | 0.868 | 19.229 | |
| preprocess_dna_mtx | 0.003 | 0.001 | 0.003 | |
| preprocess_taxa_mtx | 0.006 | 0.001 | 0.006 | |