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 12:06 -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: 2025-12-20 08:40:49 -0500 (Sat, 20 Dec 2025) |
| EndedAt: 2025-12-20 09:02:29 -0500 (Sat, 20 Dec 2025) |
| EllapsedTime: 1300.7 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 Patched (2025-11-04 r88984)
* 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 13.7.8
* 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 56.256 1.466 79.934
maaslin_plot_results 54.741 1.449 78.872
maaslin3 26.077 1.018 36.787
maaslin_contrast_test 23.574 1.271 35.162
maaslin_write_results 20.091 0.923 29.500
maaslin_write_results_lefse_format 17.346 0.810 25.082
maaslin_fit 16.007 1.455 23.907
* 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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")
2025-12-20 08:51:31.77772 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:51:33.332977 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:51:33.490891 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:51:33.51888 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:51:33.576021 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:51:33.683595 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:51:33.691596 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:51:33.725909 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:51:33.893346 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:51:33.90003 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:51:33.975777 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:51:34.068889 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:51:34.083721 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:51:34.165968 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:51:34.270168 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:52:03.306968 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:52:03.468183 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:52:03.598218 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:52:03.657373 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:52:03.757978 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:52:03.939305 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:52:03.94549 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:52:03.970927 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:52:04.181114 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:52:04.187886 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:52:04.262207 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:52:04.343394 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:52:04.358713 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:52:04.457545 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:52:04.553596 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:52:11.578 R[80339:343520812] XType: Using static font registry.
2025-12-20 08:52:48.561556 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:52:48.702965 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:52:48.793093 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:52:48.830288 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:52:48.89902 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:52:49.007236 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:52:49.014103 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:52:49.058022 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:52:49.268134 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:52:49.276082 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:52:49.333991 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:52:49.381227 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:52:49.396305 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:52:49.444562 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:52:49.647019 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:53:12.271015 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:53:12.401612 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:53:12.521596 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:53:12.550364 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:53:12.625931 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:53:12.761054 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:53:12.768855 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:53:12.795258 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:53:12.986405 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:53:12.994634 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:53:13.187324 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:53:13.230305 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:53:13.257663 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:53:13.32924 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:53:13.422822 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:53:13.747026 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/residuals_linear.rds
2025-12-20 08:53:13.907545 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/fitted_linear.rds
2025-12-20 08:53:14.037325 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/residuals_logistic.rds
2025-12-20 08:53:14.835199 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/fitted_logistic.rds
2025-12-20 08:53:53.585698 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:53:53.73819 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:53:53.892874 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:53:53.927795 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:53:53.998986 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:53:54.127208 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:53:54.134068 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:53:54.149096 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:53:54.279571 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:53:54.286747 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:53:54.372179 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:53:54.439275 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:53:54.459292 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:53:54.548812 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:53:54.676767 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:54:19.462945 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:54:19.660795 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:54:19.77369 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:54:19.804636 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:54:19.862771 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:54:19.979625 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:54:19.990781 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:54:20.013973 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:54:20.193575 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:54:20.229041 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:54:20.327471 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:54:20.39488 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:54:20.419451 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:54:20.471635 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:54:20.590004 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:54:20.932012 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/residuals_linear.rds
2025-12-20 08:54:21.071931 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/fitted_linear.rds
2025-12-20 08:54:21.206765 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/residuals_logistic.rds
2025-12-20 08:54:21.863217 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/fitted_logistic.rds
2025-12-20 08:55:00.536371 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:55:00.657668 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:55:00.790515 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:55:00.832598 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:55:00.901365 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:55:01.035057 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:55:01.049354 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:55:01.064936 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:55:01.239161 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:55:01.246512 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:55:01.332215 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:55:01.396782 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:55:01.431605 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:55:01.49681 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:55:01.630943 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:55:25.176642 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:55:25.323687 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:55:25.447229 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:55:25.510548 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:55:25.566845 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:55:25.718057 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:55:25.726028 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:55:25.740945 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:55:25.901998 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:55:25.912547 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:55:25.993654 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:55:26.07412 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:55:26.092093 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:55:26.168367 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:55:26.311097 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:55:26.674303 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/residuals_linear.rds
2025-12-20 08:55:26.804693 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/fitted_linear.rds
2025-12-20 08:55:26.935555 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/residuals_logistic.rds
2025-12-20 08:55:27.820454 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d37ef3e746/fits/fitted_logistic.rds
2025-12-20 08:56:05.528224 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:56:05.659619 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:56:05.779476 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:56:05.818273 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:56:05.88531 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:56:05.983835 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:56:05.990778 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:56:06.024635 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:56:06.197546 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:56:06.204952 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:56:06.261123 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:56:06.348752 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:56:06.367001 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:56:06.574271 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:56:06.691673 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:56:28.510462 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 08:56:28.63507 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 08:56:28.785729 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 08:56:28.856723 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 08:56:28.911602 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 08:56:29.071515 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 08:56:29.078999 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 08:56:29.097181 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 08:56:29.24218 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 08:56:29.254957 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 08:56:29.328157 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 08:56:29.398167 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 08:56:29.417149 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 08:56:29.488815 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 08:56:29.618696 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 08:57:17.686106 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 08:57:33.024456 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 08:58:20.14822 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 08:58:37.763927 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 08:58:38.756222 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_linear.rds
2025-12-20 08:58:38.898851 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_linear.rds
2025-12-20 08:58:39.025568 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_logistic.rds
2025-12-20 08:58:39.173358 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_logistic.rds
2025-12-20 08:59:20.719037 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 08:59:29.951443 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 08:59:30.553891 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_linear.rds
2025-12-20 08:59:30.711042 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_linear.rds
2025-12-20 08:59:30.814283 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_logistic.rds
2025-12-20 08:59:31.008911 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_logistic.rds
2025-12-20 09:00:04.873466 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 09:00:16.463178 WARNING::Fitting problem for feature 124 returning NA
2025-12-20 09:00:16.977812 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_linear.rds
2025-12-20 09:00:17.082491 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_linear.rds
2025-12-20 09:00:17.166336 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_logistic.rds
2025-12-20 09:00:17.331638 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_logistic.rds
2025-12-20 09:00:50.811731 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 09:00:50.960686 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 09:00:51.112723 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 09:00:51.157707 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 09:00:51.240259 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 09:00:51.388959 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 09:00:51.396523 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 09:00:51.411304 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 09:00:51.6336 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 09:00:51.643016 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 09:00:51.735465 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 09:00:51.795753 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 09:00:51.820602 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 09:00:51.908017 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 09:00:52.017552 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 09:01:13.45901 WARNING::Fitting problem for feature 50 returning NA
2025-12-20 09:01:13.657829 WARNING::Fitting problem for feature 62 returning NA
2025-12-20 09:01:13.744318 WARNING::Fitting problem for feature 74 returning NA
2025-12-20 09:01:13.797676 WARNING::Fitting problem for feature 78 returning NA
2025-12-20 09:01:13.857082 WARNING::Fitting problem for feature 84 returning NA
2025-12-20 09:01:13.97701 WARNING::Fitting problem for feature 96 returning NA
2025-12-20 09:01:13.988192 WARNING::Fitting problem for feature 97 returning NA
2025-12-20 09:01:14.015076 WARNING::Fitting problem for feature 99 returning NA
2025-12-20 09:01:14.180759 WARNING::Fitting problem for feature 114 returning NA
2025-12-20 09:01:14.196913 WARNING::Fitting problem for feature 115 returning NA
2025-12-20 09:01:14.297661 WARNING::Fitting problem for feature 123 returning NA
2025-12-20 09:01:14.367643 WARNING::Fitting problem for feature 130 returning NA
2025-12-20 09:01:14.386644 WARNING::Fitting problem for feature 132 returning NA
2025-12-20 09:01:14.46628 WARNING::Fitting problem for feature 139 returning NA
2025-12-20 09:01:14.586837 WARNING::Fitting problem for feature 150 returning NA
2025-12-20 09:01:15.022801 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_linear.rds
2025-12-20 09:01:15.152653 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_linear.rds
2025-12-20 09:01:15.316025 WARNING::Deleting existing residuals file: /tmp/Rtmpkw67hD/file139d326db797/fits/residuals_logistic.rds
2025-12-20 09:01:16.087877 WARNING::Deleting existing fitted file: /tmp/Rtmpkw67hD/file139d326db797/fits/fitted_logistic.rds
2025-12-20 09:01:52.68478 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-20 09:01:52.716176 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-20 09:01:52.736295 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-20 09:01:52.819951 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-20 09:01:52.849434 ERROR::Effect name not found in metadata: d
2025-12-20 09:01:52.873412 ERROR::No user formula provided
2025-12-20 09:01:52.92967 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-20 09:01:52.956143 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-20 09:01:57.911827 INFO::Writing function arguments to log file
2025-12-20 09:01:57.950556 INFO::Verifying options selected are valid
2025-12-20 09:02:02.080178 INFO::Writing function arguments to log file
2025-12-20 09:02:02.106129 INFO::Verifying options selected are valid
2025-12-20 09:02:02.107708 INFO::Determining format of input files
2025-12-20 09:02:02.108952 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-20 09:02:02.111807 INFO::Running selected normalization method: TSS
2025-12-20 09:02:02.113724 INFO::Creating output feature tables folder
2025-12-20 09:02:02.115302 INFO::Writing normalized data to file /tmp/Rtmpkw67hD/file139d31802294a/features/data_norm.tsv
2025-12-20 09:02:02.117509 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-20 09:02:02.118679 INFO::Total samples in data: 16
2025-12-20 09:02:02.119698 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-20 09:02:02.120619 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-20 09:02:02.122679 INFO::Total filtered features: 0
2025-12-20 09:02:02.123788 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-20 09:02:02.125075 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-20 09:02:02.126093 INFO::Filtered feature names from variance filtering:
2025-12-20 09:02:02.127097 INFO::Writing filtered data to file /tmp/Rtmpkw67hD/file139d31802294a/features/filtered_data.tsv
2025-12-20 09:02:02.128979 INFO::Running selected transform method: LOG
2025-12-20 09:02:02.130239 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpkw67hD/file139d31802294a/features/data_transformed.tsv
2025-12-20 09:02:02.134671 INFO::Applying z-score to standardize continuous metadata
2025-12-20 09:02:02.14369 INFO::Running the linear model component
2025-12-20 09:02:02.238614 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:02.259445 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:02.264719 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:02.27323 INFO::Counting total values for each feature
2025-12-20 09:02:02.275535 INFO::Running the logistic model component
2025-12-20 09:02:02.291679 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:02.309087 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:02.333079 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:02.347268 INFO::Counting total values for each feature
2025-12-20 09:02:02.36395 INFO::Re-running abundances for warn_prevalence
2025-12-20 09:02:02.371301 INFO::Running selected normalization method: TSS
2025-12-20 09:02:02.373315 INFO::Running selected transform method: LOG
2025-12-20 09:02:02.389376 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:02.402678 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:02.408479 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:02.535811 INFO::Creating fits folder
2025-12-20 09:02:02.538094 INFO::Writing residuals to file /tmp/Rtmpkw67hD/file139d31802294a/fits/residuals_linear.rds
2025-12-20 09:02:02.540094 INFO::Writing fitted values to file /tmp/Rtmpkw67hD/file139d31802294a/fits/fitted_linear.rds
2025-12-20 09:02:02.541668 INFO::Writing residuals to file /tmp/Rtmpkw67hD/file139d31802294a/fits/residuals_logistic.rds
2025-12-20 09:02:02.543147 INFO::Writing fitted values to file /tmp/Rtmpkw67hD/file139d31802294a/fits/fitted_logistic.rds
2025-12-20 09:02:02.546338 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpkw67hD/file139d31802294a/all_results.tsv
2025-12-20 09:02:02.54856 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/Rtmpkw67hD/file139d31802294a/significant_results.tsv
2025-12-20 09:02:02.577063 INFO::Creating output figures folder
2025-12-20 09:02:02.579583 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpkw67hD/file139d31802294a/figures/summary_plot.pdf
2025-12-20 09:02:05.014076 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpkw67hD/file139d31802294a/figures
2025-12-20 09:02:05.020204 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-20 09:02:05.027784 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-20 09:02:05.79883 INFO::Writing summary plot of
significant results to file: /tmp/Rtmpkw67hD/file139d31802294a/figures/summary_plot.pdf
2025-12-20 09:02:08.468748 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpkw67hD/file139d31802294a/figures
2025-12-20 09:02:08.470622 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-20 09:02:08.576078 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-20 09:02:09.505453 INFO::Running the linear model component
2025-12-20 09:02:09.514133 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:09.518766 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:09.522934 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:09.530371 INFO::Counting total values for each feature
2025-12-20 09:02:09.532327 INFO::Running the logistic model component
2025-12-20 09:02:09.594083 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:09.600784 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:09.606501 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:09.616011 INFO::Counting total values for each feature
2025-12-20 09:02:09.618345 INFO::Re-running abundances for warn_prevalence
2025-12-20 09:02:09.619159 INFO::Running selected normalization method: TSS
2025-12-20 09:02:09.620564 INFO::Running selected transform method: LOG
2025-12-20 09:02:09.628922 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:09.633513 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:09.6374 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:09.805889 INFO::Creating output folder
2025-12-20 09:02:09.807199 INFO::Creating output figures folder
2025-12-20 09:02:09.810763 INFO::Writing summary plot of significant
results to file: /tmp/Rtmpkw67hD/file139d3239cca34/figures/summary_plot.pdf
2025-12-20 09:02:12.481986 INFO::Writing association plots (one for each significant association) to output folder: /tmp/Rtmpkw67hD/file139d3239cca34/figures
2025-12-20 09:02:12.483868 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-20 09:02:12.489453 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-20 09:02:14.513508 INFO::Applying z-score to standardize continuous metadata
2025-12-20 09:02:14.528882 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-20 09:02:14.534713 INFO::Bypass z-score application to metadata
2025-12-20 09:02:14.539088 INFO::Bypass z-score application to metadata
2025-12-20 09:02:14.591567 INFO::Determining format of input files
2025-12-20 09:02:14.592767 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-20 09:02:14.593561 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-20 09:02:14.603276 INFO::Determining format of input files
2025-12-20 09:02:14.604495 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-20 09:02:14.605739 INFO::Input format is feature_specific_covariate samples as columns
2025-12-20 09:02:14.629695 INFO::Determining format of input files
2025-12-20 09:02:14.644364 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-20 09:02:14.649195 INFO::Input format is feature_specific_covariate samples as columns
2025-12-20 09:02:14.651163 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-20 09:02:14.651935 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-20 09:02:14.697583 INFO::Running selected transform method: LOG
2025-12-20 09:02:14.698957 INFO::Creating output feature tables folder
2025-12-20 09:02:14.70018 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpkw67hD/file139d32dd707fb/features/data_transformed.tsv
2025-12-20 09:02:14.705243 INFO::Running selected transform method: LOG
2025-12-20 09:02:14.706414 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpkw67hD/file139d32dd707fb/features/data_transformed.tsv
2025-12-20 09:02:14.710968 INFO::Running selected transform method: PLOG
2025-12-20 09:02:14.712696 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpkw67hD/file139d32dd707fb/features/data_transformed.tsv
2025-12-20 09:02:14.716256 INFO::Running selected transform method: NONE
2025-12-20 09:02:14.717146 INFO::Writing normalized, filtered, transformed data to file /tmp/Rtmpkw67hD/file139d32dd707fb/features/data_transformed.tsv
2025-12-20 09:02:14.738937 INFO::Running the linear model component
2025-12-20 09:02:14.747428 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:14.765818 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:14.785059 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:14.793711 INFO::Counting total values for each feature
2025-12-20 09:02:14.795658 INFO::Running the logistic model component
2025-12-20 09:02:14.803812 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:14.810518 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:14.835087 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:14.845625 INFO::Counting total values for each feature
2025-12-20 09:02:14.848039 INFO::Re-running abundances for warn_prevalence
2025-12-20 09:02:14.848926 INFO::Running selected normalization method: TSS
2025-12-20 09:02:14.852894 INFO::Running selected transform method: LOG
2025-12-20 09:02:14.862608 INFO::Fitting model to feature number 1, a
2025-12-20 09:02:14.867568 INFO::Fitting model to feature number 2, b
2025-12-20 09:02:14.873471 INFO::Fitting model to feature number 3, c
2025-12-20 09:02:15.07343 INFO::Creating output folder
2025-12-20 09:02:15.074773 INFO::Creating fits folder
2025-12-20 09:02:15.075644 INFO::Writing residuals to file /tmp/Rtmpkw67hD/file139d34d0740/fits/residuals_linear.rds
2025-12-20 09:02:15.076996 INFO::Writing fitted values to file /tmp/Rtmpkw67hD/file139d34d0740/fits/fitted_linear.rds
2025-12-20 09:02:15.079474 INFO::Writing residuals to file /tmp/Rtmpkw67hD/file139d34d0740/fits/residuals_logistic.rds
2025-12-20 09:02:15.081847 INFO::Writing fitted values to file /tmp/Rtmpkw67hD/file139d34d0740/fits/fitted_logistic.rds
2025-12-20 09:02:15.085203 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/Rtmpkw67hD/file139d34d0740/all_results.tsv
2025-12-20 09:02:15.087256 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/Rtmpkw67hD/file139d34d0740/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
459.029 10.134 662.219
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 26.077 | 1.018 | 36.787 | |
| maaslin_check_arguments | 0.230 | 0.004 | 0.290 | |
| maaslin_check_formula | 0.194 | 0.010 | 0.286 | |
| maaslin_compute_formula | 0.207 | 0.011 | 0.336 | |
| maaslin_contrast_test | 23.574 | 1.271 | 35.162 | |
| maaslin_filter | 0.710 | 0.054 | 1.040 | |
| maaslin_fit | 16.007 | 1.455 | 23.907 | |
| maaslin_log_arguments | 0.201 | 0.010 | 0.254 | |
| maaslin_normalize | 0.414 | 0.029 | 0.626 | |
| maaslin_plot_results | 54.741 | 1.449 | 78.872 | |
| maaslin_plot_results_from_output | 56.256 | 1.466 | 79.934 | |
| maaslin_process_metadata | 0.738 | 0.052 | 1.030 | |
| maaslin_read_data | 0.181 | 0.009 | 0.229 | |
| maaslin_reorder_data | 0.191 | 0.010 | 0.337 | |
| maaslin_transform | 0.920 | 0.071 | 1.387 | |
| maaslin_write_results | 20.091 | 0.923 | 29.500 | |
| maaslin_write_results_lefse_format | 17.346 | 0.810 | 25.082 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.023 | 0.001 | 0.033 | |