William Nickols
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 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 2025-12-22 12:04 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 2025-12-19 06:24:57 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 06:54:24 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 1766.8 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 4.5.2 (2025-10-31)
* 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 102.520 1.649 109.283
maaslin_plot_results_from_output 101.522 1.218 106.720
maaslin_contrast_test 42.444 1.700 47.341
maaslin3 41.585 1.617 46.268
maaslin_write_results_lefse_format 37.490 0.962 38.724
maaslin_write_results 31.602 1.152 33.341
maaslin_fit 30.569 0.959 33.687
* 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2025-12-19 06:39:10.494288 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:39:11.429654 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:39:11.65592 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:39:11.713263 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:39:11.813358 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:39:12.035118 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:39:12.05041 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:39:12.099443 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:39:12.471245 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:39:12.529908 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:39:12.677358 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:39:12.795772 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:39:12.828268 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:39:12.988909 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:39:13.200738 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:39:46.602152 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:39:46.812047 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:39:47.018458 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:39:47.078087 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:39:47.177264 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:39:47.415847 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:39:47.431069 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:39:47.463829 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:39:47.721421 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:39:47.736297 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:39:47.883884 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:39:47.99683 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:39:48.030403 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:39:48.14958 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:39:48.343316 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:39:57.572 R[59564:143506928] XType: com.apple.fonts is not accessible.
2025-12-19 06:39:57.573 R[59564:143506928] XType: XTFontStaticRegistry is enabled.
2025-12-19 06:40:43.758316 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:40:43.968744 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:40:44.173846 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:40:44.237097 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:40:44.33016 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:40:44.530199 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:40:44.544373 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:40:44.575632 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:40:45.835745 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:40:45.850229 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:40:45.987448 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:40:46.094337 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:40:46.14437 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:40:46.255689 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:40:46.453419 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:41:16.221961 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:41:16.482699 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:41:16.685106 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:41:16.745765 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:41:16.84521 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:41:17.056825 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:41:17.071346 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:41:17.103672 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:41:17.361525 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:41:17.376874 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:41:17.513688 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:41:17.625225 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:41:17.656369 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:41:17.768523 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:41:17.958776 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:41:18.487083 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/residuals_linear.rds
2025-12-19 06:41:18.593671 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/fitted_linear.rds
2025-12-19 06:41:18.702536 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/residuals_logistic.rds
2025-12-19 06:41:19.287519 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/fitted_logistic.rds
2025-12-19 06:42:09.430485 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:42:09.673527 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:42:09.881206 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:42:09.941315 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:42:10.035028 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:42:10.235419 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:42:10.249525 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:42:10.282074 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:42:10.541179 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:42:10.556475 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:42:10.702051 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:42:10.815694 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:42:10.849009 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:42:10.96593 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:42:11.159412 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:42:40.326767 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:42:40.523748 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:42:40.787427 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:42:40.84565 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:42:40.94253 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:42:41.126783 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:42:41.139575 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:42:41.169184 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:42:41.42561 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:42:41.44055 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:42:41.570738 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:42:41.680418 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:42:41.712248 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:42:41.82381 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:42:42.014147 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:42:42.570451 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/residuals_linear.rds
2025-12-19 06:42:42.676901 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/fitted_linear.rds
2025-12-19 06:42:42.822055 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/residuals_logistic.rds
2025-12-19 06:42:43.400256 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/fitted_logistic.rds
2025-12-19 06:43:32.943717 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:43:33.153667 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:43:33.366486 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:43:33.427528 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:43:33.524701 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:43:33.747319 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:43:33.761674 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:43:33.793928 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:43:34.067084 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:43:34.08239 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:43:34.227257 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:43:34.338561 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:43:34.369827 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:43:34.484668 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:43:34.678703 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:44:05.420659 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:44:05.636683 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:44:05.833342 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:44:05.893084 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:44:05.989299 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:44:06.254403 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:44:06.268425 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:44:06.300164 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:44:06.555448 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:44:06.569711 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:44:06.70344 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:44:06.808772 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:44:06.840807 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:44:06.985138 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:44:07.170202 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:44:07.688121 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/residuals_linear.rds
2025-12-19 06:44:07.794917 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/fitted_linear.rds
2025-12-19 06:44:07.904396 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/residuals_logistic.rds
2025-12-19 06:44:08.475714 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac3b49e171/fits/fitted_logistic.rds
2025-12-19 06:44:57.637479 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:44:57.850095 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:44:58.051512 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:44:58.110564 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:44:58.201196 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:44:58.410084 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:44:58.424928 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:44:58.458727 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:44:58.720625 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:44:58.73506 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:44:58.86985 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:44:58.983409 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:44:59.014399 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:44:59.125462 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:44:59.353542 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:45:30.068396 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:45:30.307591 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:45:30.534078 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:45:30.595141 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:45:30.693795 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:45:30.915415 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:45:30.935316 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:45:30.970629 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:45:31.276545 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:45:31.295202 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:45:31.454153 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:45:31.579212 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:45:31.624211 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:45:31.745864 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:45:31.940708 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:46:35.640404 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:46:59.741991 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:48:05.072594 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:48:28.176787 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:48:29.886232 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_linear.rds
2025-12-19 06:48:30.004986 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_linear.rds
2025-12-19 06:48:30.076406 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_logistic.rds
2025-12-19 06:48:30.232746 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_logistic.rds
2025-12-19 06:49:30.818863 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:49:44.434615 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:49:45.324052 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_linear.rds
2025-12-19 06:49:45.444648 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_linear.rds
2025-12-19 06:49:45.52654 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_logistic.rds
2025-12-19 06:49:45.672748 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_logistic.rds
2025-12-19 06:50:36.418805 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:50:52.146493 WARNING::Fitting problem for feature 124 returning NA
2025-12-19 06:50:53.197576 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_linear.rds
2025-12-19 06:50:53.334701 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_linear.rds
2025-12-19 06:50:53.416018 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_logistic.rds
2025-12-19 06:50:53.579129 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_logistic.rds
2025-12-19 06:51:42.279862 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:51:42.499202 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:51:42.734581 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:51:42.801945 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:51:42.907012 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:51:43.150176 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:51:43.169471 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:51:43.208439 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:51:43.510652 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:51:43.525494 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:51:43.685175 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:51:43.811916 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:51:43.845447 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:51:43.96906 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:51:44.182378 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:52:19.501001 WARNING::Fitting problem for feature 50 returning NA
2025-12-19 06:52:19.80985 WARNING::Fitting problem for feature 62 returning NA
2025-12-19 06:52:20.081716 WARNING::Fitting problem for feature 74 returning NA
2025-12-19 06:52:20.166265 WARNING::Fitting problem for feature 78 returning NA
2025-12-19 06:52:20.296787 WARNING::Fitting problem for feature 84 returning NA
2025-12-19 06:52:20.589896 WARNING::Fitting problem for feature 96 returning NA
2025-12-19 06:52:20.606396 WARNING::Fitting problem for feature 97 returning NA
2025-12-19 06:52:20.651326 WARNING::Fitting problem for feature 99 returning NA
2025-12-19 06:52:21.005664 WARNING::Fitting problem for feature 114 returning NA
2025-12-19 06:52:21.028079 WARNING::Fitting problem for feature 115 returning NA
2025-12-19 06:52:21.209448 WARNING::Fitting problem for feature 123 returning NA
2025-12-19 06:52:21.364674 WARNING::Fitting problem for feature 130 returning NA
2025-12-19 06:52:21.407886 WARNING::Fitting problem for feature 132 returning NA
2025-12-19 06:52:21.550992 WARNING::Fitting problem for feature 139 returning NA
2025-12-19 06:52:21.828142 WARNING::Fitting problem for feature 150 returning NA
2025-12-19 06:52:22.859668 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_linear.rds
2025-12-19 06:52:23.010128 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_linear.rds
2025-12-19 06:52:23.155108 WARNING::Deleting existing residuals file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/residuals_logistic.rds
2025-12-19 06:52:23.931246 WARNING::Deleting existing fitted file: /tmp/RtmpT1pXQT/filee8ac1161eef6/fits/fitted_logistic.rds
2025-12-19 06:53:23.94068 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-19 06:53:24.003371 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-19 06:53:24.046961 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-19 06:53:24.229811 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-19 06:53:24.289597 ERROR::Effect name not found in metadata: d
2025-12-19 06:53:24.329978 ERROR::No user formula provided
2025-12-19 06:53:24.435694 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-19 06:53:24.478369 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-19 06:53:36.466117 INFO::Writing function arguments to log file
2025-12-19 06:53:36.527435 INFO::Verifying options selected are valid
2025-12-19 06:53:43.97113 INFO::Writing function arguments to log file
2025-12-19 06:53:44.023307 INFO::Verifying options selected are valid
2025-12-19 06:53:44.026132 INFO::Determining format of input files
2025-12-19 06:53:44.028908 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-19 06:53:44.038655 INFO::Running selected normalization method: TSS
2025-12-19 06:53:44.042364 INFO::Creating output feature tables folder
2025-12-19 06:53:44.045085 INFO::Writing normalized data to file /tmp/RtmpT1pXQT/filee8acad18746/features/data_norm.tsv
2025-12-19 06:53:44.053438 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-19 06:53:44.055935 INFO::Total samples in data: 16
2025-12-19 06:53:44.058379 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-19 06:53:44.065161 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-19 06:53:44.0706 INFO::Total filtered features: 0
2025-12-19 06:53:44.073692 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-19 06:53:44.078501 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-19 06:53:44.081163 INFO::Filtered feature names from variance filtering:
2025-12-19 06:53:44.083749 INFO::Writing filtered data to file /tmp/RtmpT1pXQT/filee8acad18746/features/filtered_data.tsv
2025-12-19 06:53:44.088476 INFO::Running selected transform method: LOG
2025-12-19 06:53:44.09187 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT1pXQT/filee8acad18746/features/data_transformed.tsv
2025-12-19 06:53:44.098988 INFO::Applying z-score to standardize continuous metadata
2025-12-19 06:53:44.117485 INFO::Running the linear model component
2025-12-19 06:53:44.1754 INFO::Fitting model to feature number 1, a
2025-12-19 06:53:44.189775 INFO::Fitting model to feature number 2, b
2025-12-19 06:53:44.209111 INFO::Fitting model to feature number 3, c
2025-12-19 06:53:44.233099 INFO::Counting total values for each feature
2025-12-19 06:53:44.24353 INFO::Running the logistic model component
2025-12-19 06:53:44.299931 INFO::Fitting model to feature number 1, a
2025-12-19 06:53:44.323739 INFO::Fitting model to feature number 2, b
2025-12-19 06:53:44.343802 INFO::Fitting model to feature number 3, c
2025-12-19 06:53:44.370182 INFO::Counting total values for each feature
2025-12-19 06:53:44.382132 INFO::Re-running abundances for warn_prevalence
2025-12-19 06:53:44.384947 INFO::Running selected normalization method: TSS
2025-12-19 06:53:44.391633 INFO::Running selected transform method: LOG
2025-12-19 06:53:44.444618 INFO::Fitting model to feature number 1, a
2025-12-19 06:53:44.462515 INFO::Fitting model to feature number 2, b
2025-12-19 06:53:44.479529 INFO::Fitting model to feature number 3, c
2025-12-19 06:53:44.774599 INFO::Creating fits folder
2025-12-19 06:53:44.777633 INFO::Writing residuals to file /tmp/RtmpT1pXQT/filee8acad18746/fits/residuals_linear.rds
2025-12-19 06:53:44.780967 INFO::Writing fitted values to file /tmp/RtmpT1pXQT/filee8acad18746/fits/fitted_linear.rds
2025-12-19 06:53:44.789121 INFO::Writing residuals to file /tmp/RtmpT1pXQT/filee8acad18746/fits/residuals_logistic.rds
2025-12-19 06:53:44.792441 INFO::Writing fitted values to file /tmp/RtmpT1pXQT/filee8acad18746/fits/fitted_logistic.rds
2025-12-19 06:53:44.801217 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpT1pXQT/filee8acad18746/all_results.tsv
2025-12-19 06:53:44.806129 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/RtmpT1pXQT/filee8acad18746/significant_results.tsv
2025-12-19 06:53:44.81338 INFO::Creating output figures folder
2025-12-19 06:53:44.817797 INFO::Writing summary plot of significant
results to file: /tmp/RtmpT1pXQT/filee8acad18746/figures/summary_plot.pdf
2025-12-19 06:53:49.926592 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpT1pXQT/filee8acad18746/figures
2025-12-19 06:53:49.930899 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-19 06:53:49.945293 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-19 06:53:51.355986 INFO::Writing summary plot of
significant results to file: /tmp/RtmpT1pXQT/filee8acad18746/figures/summary_plot.pdf
2025-12-19 06:53:55.57091 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpT1pXQT/filee8acad18746/figures
2025-12-19 06:53:55.575361 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-19 06:53:55.587544 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-19 06:53:56.942715 INFO::Running the linear model component
2025-12-19 06:53:56.969793 INFO::Fitting model to feature number 1, a
2025-12-19 06:53:56.983545 INFO::Fitting model to feature number 2, b
2025-12-19 06:53:56.995384 INFO::Fitting model to feature number 3, c
2025-12-19 06:53:57.015156 INFO::Counting total values for each feature
2025-12-19 06:53:57.021895 INFO::Running the logistic model component
2025-12-19 06:53:57.051867 INFO::Fitting model to feature number 1, a
2025-12-19 06:53:57.071092 INFO::Fitting model to feature number 2, b
2025-12-19 06:53:57.089607 INFO::Fitting model to feature number 3, c
2025-12-19 06:53:57.123629 INFO::Counting total values for each feature
2025-12-19 06:53:57.128705 INFO::Re-running abundances for warn_prevalence
2025-12-19 06:53:57.130652 INFO::Running selected normalization method: TSS
2025-12-19 06:53:57.137422 INFO::Running selected transform method: LOG
2025-12-19 06:53:57.165361 INFO::Fitting model to feature number 1, a
2025-12-19 06:53:57.176677 INFO::Fitting model to feature number 2, b
2025-12-19 06:53:57.189044 INFO::Fitting model to feature number 3, c
2025-12-19 06:53:57.460257 INFO::Creating output folder
2025-12-19 06:53:57.462642 INFO::Creating output figures folder
2025-12-19 06:53:57.46593 INFO::Writing summary plot of significant
results to file: /tmp/RtmpT1pXQT/filee8ac6db55df5/figures/summary_plot.pdf
2025-12-19 06:54:02.182138 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpT1pXQT/filee8ac6db55df5/figures
2025-12-19 06:54:02.186138 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-19 06:54:02.198915 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-19 06:54:05.402068 INFO::Applying z-score to standardize continuous metadata
2025-12-19 06:54:05.420487 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-19 06:54:05.4229 INFO::Bypass z-score application to metadata
2025-12-19 06:54:05.429362 INFO::Bypass z-score application to metadata
2025-12-19 06:54:05.482092 INFO::Determining format of input files
2025-12-19 06:54:05.484294 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-19 06:54:05.488093 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-19 06:54:05.509737 INFO::Determining format of input files
2025-12-19 06:54:05.512329 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-19 06:54:05.515647 INFO::Input format is feature_specific_covariate samples as columns
2025-12-19 06:54:05.540532 INFO::Determining format of input files
2025-12-19 06:54:05.543739 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-19 06:54:05.546501 INFO::Input format is feature_specific_covariate samples as columns
2025-12-19 06:54:05.550628 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-19 06:54:05.553203 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-19 06:54:05.586454 INFO::Running selected transform method: LOG
2025-12-19 06:54:05.590466 INFO::Creating output feature tables folder
2025-12-19 06:54:05.592931 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT1pXQT/filee8ac36e5b497/features/data_transformed.tsv
2025-12-19 06:54:05.60349 INFO::Running selected transform method: LOG
2025-12-19 06:54:05.606556 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT1pXQT/filee8ac36e5b497/features/data_transformed.tsv
2025-12-19 06:54:05.618179 INFO::Running selected transform method: PLOG
2025-12-19 06:54:05.623124 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT1pXQT/filee8ac36e5b497/features/data_transformed.tsv
2025-12-19 06:54:05.632698 INFO::Running selected transform method: NONE
2025-12-19 06:54:05.6356 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpT1pXQT/filee8ac36e5b497/features/data_transformed.tsv
2025-12-19 06:54:05.657062 INFO::Running the linear model component
2025-12-19 06:54:05.68098 INFO::Fitting model to feature number 1, a
2025-12-19 06:54:05.692389 INFO::Fitting model to feature number 2, b
2025-12-19 06:54:05.703002 INFO::Fitting model to feature number 3, c
2025-12-19 06:54:05.721819 INFO::Counting total values for each feature
2025-12-19 06:54:05.726091 INFO::Running the logistic model component
2025-12-19 06:54:05.75104 INFO::Fitting model to feature number 1, a
2025-12-19 06:54:05.77369 INFO::Fitting model to feature number 2, b
2025-12-19 06:54:05.79115 INFO::Fitting model to feature number 3, c
2025-12-19 06:54:05.815531 INFO::Counting total values for each feature
2025-12-19 06:54:05.820706 INFO::Re-running abundances for warn_prevalence
2025-12-19 06:54:05.82267 INFO::Running selected normalization method: TSS
2025-12-19 06:54:05.826035 INFO::Running selected transform method: LOG
2025-12-19 06:54:05.852731 INFO::Fitting model to feature number 1, a
2025-12-19 06:54:05.866476 INFO::Fitting model to feature number 2, b
2025-12-19 06:54:05.880044 INFO::Fitting model to feature number 3, c
2025-12-19 06:54:06.159647 INFO::Creating output folder
2025-12-19 06:54:06.162304 INFO::Creating fits folder
2025-12-19 06:54:06.164562 INFO::Writing residuals to file /tmp/RtmpT1pXQT/filee8ac22b341a9/fits/residuals_linear.rds
2025-12-19 06:54:06.168429 INFO::Writing fitted values to file /tmp/RtmpT1pXQT/filee8ac22b341a9/fits/fitted_linear.rds
2025-12-19 06:54:06.171444 INFO::Writing residuals to file /tmp/RtmpT1pXQT/filee8ac22b341a9/fits/residuals_logistic.rds
2025-12-19 06:54:06.174052 INFO::Writing fitted values to file /tmp/RtmpT1pXQT/filee8ac22b341a9/fits/fitted_logistic.rds
2025-12-19 06:54:06.186437 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpT1pXQT/filee8ac22b341a9/all_results.tsv
2025-12-19 06:54:06.191183 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/RtmpT1pXQT/filee8ac22b341a9/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
812.696 12.826 918.496
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 41.585 | 1.617 | 46.268 | |
| maaslin_check_arguments | 0.280 | 0.007 | 0.298 | |
| maaslin_check_formula | 0.300 | 0.014 | 0.315 | |
| maaslin_compute_formula | 0.310 | 0.017 | 0.366 | |
| maaslin_contrast_test | 42.444 | 1.700 | 47.341 | |
| maaslin_filter | 1.265 | 0.091 | 1.426 | |
| maaslin_fit | 30.569 | 0.959 | 33.687 | |
| maaslin_log_arguments | 0.288 | 0.015 | 0.320 | |
| maaslin_normalize | 0.756 | 0.065 | 0.905 | |
| maaslin_plot_results | 102.520 | 1.649 | 109.283 | |
| maaslin_plot_results_from_output | 101.522 | 1.218 | 106.720 | |
| maaslin_process_metadata | 1.327 | 0.083 | 1.499 | |
| maaslin_read_data | 0.293 | 0.015 | 0.328 | |
| maaslin_reorder_data | 0.309 | 0.014 | 0.324 | |
| maaslin_transform | 2.637 | 0.232 | 2.890 | |
| maaslin_write_results | 31.602 | 1.152 | 33.341 | |
| maaslin_write_results_lefse_format | 37.490 | 0.962 | 38.724 | |
| preprocess_dna_mtx | 0.008 | 0.001 | 0.009 | |
| preprocess_taxa_mtx | 0.010 | 0.001 | 0.011 | |