William Nickols
| Snapshot Date: 2025-12-15 13:45 -0500 (Mon, 15 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 2025-12-18 12:06 -0500 (Thu, 18 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" | 4882 |
| 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: 2025-12-17 08:39:26 -0500 (Wed, 17 Dec 2025) |
| EndedAt: 2025-12-17 09:01:04 -0500 (Wed, 17 Dec 2025) |
| EllapsedTime: 1297.9 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 55.171 1.309 78.857
maaslin_plot_results 54.528 1.564 77.956
maaslin3 27.789 1.065 39.784
maaslin_contrast_test 22.712 1.336 33.265
maaslin_write_results 18.838 1.082 27.098
maaslin_write_results_lefse_format 17.501 0.891 26.173
maaslin_fit 15.483 0.582 21.897
* 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")
2025-12-17 08:50:07.355467 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:50:08.743395 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:50:08.876992 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:50:08.909813 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:50:08.968113 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:50:09.11322 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:50:09.121788 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:50:09.154951 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:50:09.32628 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:50:09.345321 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:50:09.433342 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:50:09.514108 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:50:09.540578 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:50:09.631715 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:50:09.732469 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:50:38.819037 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:50:38.949757 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:50:39.095979 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:50:39.136645 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:50:39.218964 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:50:39.377944 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:50:39.392014 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:50:39.442536 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:50:39.559409 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:50:39.568987 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:50:39.644029 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:50:39.698181 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:50:39.716671 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:50:39.792173 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:50:39.936939 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:50:46.972 R[1594:303177230] XType: Using static font registry.
2025-12-17 08:51:23.943443 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:51:24.097517 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:51:24.224314 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:51:24.281378 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:51:24.363985 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:51:24.508853 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:51:24.515723 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:51:24.531827 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:51:24.797175 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:51:24.814918 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:51:24.92968 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:51:25.02096 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:51:25.046205 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:51:25.107484 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:51:25.250072 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:51:48.663332 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:51:48.780076 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:51:48.905152 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:51:48.936603 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:51:48.991349 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:51:49.14048 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:51:49.157628 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:51:49.175623 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:51:49.326386 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:51:49.337545 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:51:49.425347 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:51:49.492329 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:51:49.521048 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:51:49.573256 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:51:49.6742 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:51:50.013218 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a3375c626/fits/residuals_linear.rds
2025-12-17 08:51:50.153945 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a3375c626/fits/fitted_linear.rds
2025-12-17 08:51:50.32217 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a3375c626/fits/residuals_logistic.rds
2025-12-17 08:51:51.026426 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a3375c626/fits/fitted_logistic.rds
2025-12-17 08:52:28.787997 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:52:28.924202 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:52:29.071947 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:52:29.111128 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:52:29.203769 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:52:29.306514 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:52:29.313426 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:52:29.327935 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:52:29.558458 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:52:29.56557 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:52:29.639112 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:52:29.712154 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:52:29.730327 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:52:29.824615 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:52:29.964097 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:52:54.697957 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:52:54.865522 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:52:55.034397 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:52:55.102707 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:52:55.190632 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:52:55.337612 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:52:55.344326 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:52:55.380251 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:52:55.583061 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:52:55.596893 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:52:55.733632 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:52:55.856802 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:52:55.889594 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:52:55.934944 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:52:56.127107 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:52:56.435799 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a3375c626/fits/residuals_linear.rds
2025-12-17 08:52:56.553509 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a3375c626/fits/fitted_linear.rds
2025-12-17 08:52:56.683435 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a3375c626/fits/residuals_logistic.rds
2025-12-17 08:52:57.302563 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a3375c626/fits/fitted_logistic.rds
2025-12-17 08:53:35.220191 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:53:35.337177 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:53:35.451602 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:53:35.486935 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:53:35.538291 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:53:35.662147 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:53:35.669038 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:53:35.691541 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:53:35.87079 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:53:35.878155 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:53:35.991756 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:53:36.063266 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:53:36.078222 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:53:36.145218 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:53:36.303434 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:53:59.211284 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:53:59.378028 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:53:59.513065 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:53:59.556872 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:53:59.604746 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:53:59.735867 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:53:59.74323 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:53:59.778916 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:53:59.927233 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:53:59.934364 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:54:00.055787 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:54:00.138553 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:54:00.155896 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:54:00.217172 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:54:00.347505 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:54:00.667645 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a3375c626/fits/residuals_linear.rds
2025-12-17 08:54:00.820078 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a3375c626/fits/fitted_linear.rds
2025-12-17 08:54:00.965219 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a3375c626/fits/residuals_logistic.rds
2025-12-17 08:54:01.760666 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a3375c626/fits/fitted_logistic.rds
2025-12-17 08:54:40.481816 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:54:40.59586 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:54:40.762374 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:54:40.798203 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:54:40.845798 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:54:40.973151 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:54:40.992552 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:54:41.013629 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:54:41.184142 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:54:41.203908 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:54:41.292072 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:54:41.353623 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:54:41.376196 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:54:41.431388 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:54:41.529152 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:55:02.722637 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:55:02.842509 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:55:03.000905 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:55:03.035793 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:55:03.086767 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:55:03.230628 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:55:03.238782 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:55:03.253275 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:55:03.424527 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:55:03.432138 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:55:03.523467 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:55:03.606559 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:55:03.633733 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:55:03.728421 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:55:03.858259 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:55:50.489407 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:56:05.15598 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:56:52.988219 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:57:11.189171 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:57:12.14826 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_linear.rds
2025-12-17 08:57:12.282364 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_linear.rds
2025-12-17 08:57:12.368539 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_logistic.rds
2025-12-17 08:57:12.525449 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_logistic.rds
2025-12-17 08:57:54.459308 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:58:03.710691 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:58:04.214523 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_linear.rds
2025-12-17 08:58:04.33626 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_linear.rds
2025-12-17 08:58:04.42805 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_logistic.rds
2025-12-17 08:58:04.581145 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_logistic.rds
2025-12-17 08:58:38.888642 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:58:51.385581 WARNING::Fitting problem for feature 124 returning NA
2025-12-17 08:58:51.993399 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_linear.rds
2025-12-17 08:58:52.121747 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_linear.rds
2025-12-17 08:58:52.216143 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_logistic.rds
2025-12-17 08:58:52.361716 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_logistic.rds
2025-12-17 08:59:25.867019 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:59:26.04879 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:59:26.237929 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:59:26.263479 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:59:26.302818 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:59:26.457905 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:59:26.468422 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:59:26.481952 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:59:26.641183 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:59:26.64788 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:59:26.732091 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:59:26.808732 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:59:26.847284 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:59:26.912227 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:59:27.072467 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:59:48.664214 WARNING::Fitting problem for feature 50 returning NA
2025-12-17 08:59:48.795153 WARNING::Fitting problem for feature 62 returning NA
2025-12-17 08:59:48.90589 WARNING::Fitting problem for feature 74 returning NA
2025-12-17 08:59:48.933251 WARNING::Fitting problem for feature 78 returning NA
2025-12-17 08:59:48.98859 WARNING::Fitting problem for feature 84 returning NA
2025-12-17 08:59:49.137876 WARNING::Fitting problem for feature 96 returning NA
2025-12-17 08:59:49.144992 WARNING::Fitting problem for feature 97 returning NA
2025-12-17 08:59:49.168785 WARNING::Fitting problem for feature 99 returning NA
2025-12-17 08:59:49.367426 WARNING::Fitting problem for feature 114 returning NA
2025-12-17 08:59:49.374646 WARNING::Fitting problem for feature 115 returning NA
2025-12-17 08:59:49.471013 WARNING::Fitting problem for feature 123 returning NA
2025-12-17 08:59:49.519827 WARNING::Fitting problem for feature 130 returning NA
2025-12-17 08:59:49.544833 WARNING::Fitting problem for feature 132 returning NA
2025-12-17 08:59:49.651458 WARNING::Fitting problem for feature 139 returning NA
2025-12-17 08:59:49.759321 WARNING::Fitting problem for feature 150 returning NA
2025-12-17 08:59:50.156852 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_linear.rds
2025-12-17 08:59:50.312682 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_linear.rds
2025-12-17 08:59:50.456476 WARNING::Deleting existing residuals file: /tmp/RtmpW5dEye/file63a55741871/fits/residuals_logistic.rds
2025-12-17 08:59:51.173238 WARNING::Deleting existing fitted file: /tmp/RtmpW5dEye/file63a55741871/fits/fitted_logistic.rds
2025-12-17 09:00:27.231002 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-17 09:00:27.286673 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-17 09:00:27.313972 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-17 09:00:27.393413 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-17 09:00:27.416402 ERROR::Effect name not found in metadata: d
2025-12-17 09:00:27.43612 ERROR::No user formula provided
2025-12-17 09:00:27.483519 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-17 09:00:27.511982 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-17 09:00:32.748264 INFO::Writing function arguments to log file
2025-12-17 09:00:32.776631 INFO::Verifying options selected are valid
2025-12-17 09:00:36.836482 INFO::Writing function arguments to log file
2025-12-17 09:00:36.851018 INFO::Verifying options selected are valid
2025-12-17 09:00:36.85229 INFO::Determining format of input files
2025-12-17 09:00:36.853253 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-17 09:00:36.855728 INFO::Running selected normalization method: TSS
2025-12-17 09:00:36.857366 INFO::Creating output feature tables folder
2025-12-17 09:00:36.871027 INFO::Writing normalized data to file /tmp/RtmpW5dEye/file63a2e10ed4/features/data_norm.tsv
2025-12-17 09:00:36.877124 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-17 09:00:36.878459 INFO::Total samples in data: 16
2025-12-17 09:00:36.879467 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-17 09:00:36.880442 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-17 09:00:36.885482 INFO::Total filtered features: 0
2025-12-17 09:00:36.88688 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-17 09:00:36.888211 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-17 09:00:36.889233 INFO::Filtered feature names from variance filtering:
2025-12-17 09:00:36.890177 INFO::Writing filtered data to file /tmp/RtmpW5dEye/file63a2e10ed4/features/filtered_data.tsv
2025-12-17 09:00:36.892064 INFO::Running selected transform method: LOG
2025-12-17 09:00:36.89334 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpW5dEye/file63a2e10ed4/features/data_transformed.tsv
2025-12-17 09:00:36.895316 INFO::Applying z-score to standardize continuous metadata
2025-12-17 09:00:36.901322 INFO::Running the linear model component
2025-12-17 09:00:36.917234 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:36.927672 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:36.93761 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:36.952149 INFO::Counting total values for each feature
2025-12-17 09:00:36.954815 INFO::Running the logistic model component
2025-12-17 09:00:36.98245 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:36.992482 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:37.006426 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:37.018161 INFO::Counting total values for each feature
2025-12-17 09:00:37.023961 INFO::Re-running abundances for warn_prevalence
2025-12-17 09:00:37.025578 INFO::Running selected normalization method: TSS
2025-12-17 09:00:37.027475 INFO::Running selected transform method: LOG
2025-12-17 09:00:37.044617 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:37.086051 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:37.09243 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:37.245084 INFO::Creating fits folder
2025-12-17 09:00:37.247141 INFO::Writing residuals to file /tmp/RtmpW5dEye/file63a2e10ed4/fits/residuals_linear.rds
2025-12-17 09:00:37.24898 INFO::Writing fitted values to file /tmp/RtmpW5dEye/file63a2e10ed4/fits/fitted_linear.rds
2025-12-17 09:00:37.25956 INFO::Writing residuals to file /tmp/RtmpW5dEye/file63a2e10ed4/fits/residuals_logistic.rds
2025-12-17 09:00:37.263232 INFO::Writing fitted values to file /tmp/RtmpW5dEye/file63a2e10ed4/fits/fitted_logistic.rds
2025-12-17 09:00:37.267087 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpW5dEye/file63a2e10ed4/all_results.tsv
2025-12-17 09:00:37.269637 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/RtmpW5dEye/file63a2e10ed4/significant_results.tsv
2025-12-17 09:00:37.271669 INFO::Creating output figures folder
2025-12-17 09:00:37.273695 INFO::Writing summary plot of significant
results to file: /tmp/RtmpW5dEye/file63a2e10ed4/figures/summary_plot.pdf
2025-12-17 09:00:39.95215 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpW5dEye/file63a2e10ed4/figures
2025-12-17 09:00:39.96064 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-17 09:00:39.988039 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-17 09:00:40.911652 INFO::Writing summary plot of
significant results to file: /tmp/RtmpW5dEye/file63a2e10ed4/figures/summary_plot.pdf
2025-12-17 09:00:43.540725 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpW5dEye/file63a2e10ed4/figures
2025-12-17 09:00:43.542528 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-17 09:00:43.565228 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-17 09:00:44.283943 INFO::Running the linear model component
2025-12-17 09:00:44.297655 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:44.302613 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:44.30687 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:44.314658 INFO::Counting total values for each feature
2025-12-17 09:00:44.316547 INFO::Running the logistic model component
2025-12-17 09:00:44.326825 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:44.343136 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:44.346307 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:44.360417 INFO::Counting total values for each feature
2025-12-17 09:00:44.362548 INFO::Re-running abundances for warn_prevalence
2025-12-17 09:00:44.363001 INFO::Running selected normalization method: TSS
2025-12-17 09:00:44.364001 INFO::Running selected transform method: LOG
2025-12-17 09:00:44.373577 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:44.382318 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:44.386447 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:44.527234 INFO::Creating output folder
2025-12-17 09:00:44.528684 INFO::Creating output figures folder
2025-12-17 09:00:44.532114 INFO::Writing summary plot of significant
results to file: /tmp/RtmpW5dEye/file63a4274ee79/figures/summary_plot.pdf
2025-12-17 09:00:47.258989 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpW5dEye/file63a4274ee79/figures
2025-12-17 09:00:47.260844 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-17 09:00:47.266575 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-17 09:00:49.304336 INFO::Applying z-score to standardize continuous metadata
2025-12-17 09:00:49.320778 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-17 09:00:49.321814 INFO::Bypass z-score application to metadata
2025-12-17 09:00:49.324586 INFO::Bypass z-score application to metadata
2025-12-17 09:00:49.347211 INFO::Determining format of input files
2025-12-17 09:00:49.348393 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-17 09:00:49.3492 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-17 09:00:49.373349 INFO::Determining format of input files
2025-12-17 09:00:49.374739 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-17 09:00:49.376059 INFO::Input format is feature_specific_covariate samples as columns
2025-12-17 09:00:49.384865 INFO::Determining format of input files
2025-12-17 09:00:49.385954 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-17 09:00:49.386953 INFO::Input format is feature_specific_covariate samples as columns
2025-12-17 09:00:49.38846 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-17 09:00:49.38916 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-17 09:00:49.401978 INFO::Running selected transform method: LOG
2025-12-17 09:00:49.403235 INFO::Creating output feature tables folder
2025-12-17 09:00:49.404339 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpW5dEye/file63a700d8056/features/data_transformed.tsv
2025-12-17 09:00:49.40895 INFO::Running selected transform method: LOG
2025-12-17 09:00:49.410179 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpW5dEye/file63a700d8056/features/data_transformed.tsv
2025-12-17 09:00:49.420883 INFO::Running selected transform method: PLOG
2025-12-17 09:00:49.425994 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpW5dEye/file63a700d8056/features/data_transformed.tsv
2025-12-17 09:00:49.43034 INFO::Running selected transform method: NONE
2025-12-17 09:00:49.431299 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpW5dEye/file63a700d8056/features/data_transformed.tsv
2025-12-17 09:00:49.455916 INFO::Running the linear model component
2025-12-17 09:00:49.46455 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:49.469201 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:49.475054 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:49.485171 INFO::Counting total values for each feature
2025-12-17 09:00:49.487039 INFO::Running the logistic model component
2025-12-17 09:00:49.495519 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:49.518004 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:49.524455 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:49.550722 INFO::Counting total values for each feature
2025-12-17 09:00:49.553235 INFO::Re-running abundances for warn_prevalence
2025-12-17 09:00:49.554097 INFO::Running selected normalization method: TSS
2025-12-17 09:00:49.555687 INFO::Running selected transform method: LOG
2025-12-17 09:00:49.56451 INFO::Fitting model to feature number 1, a
2025-12-17 09:00:49.571801 INFO::Fitting model to feature number 2, b
2025-12-17 09:00:49.576485 INFO::Fitting model to feature number 3, c
2025-12-17 09:00:49.698298 INFO::Creating output folder
2025-12-17 09:00:49.699662 INFO::Creating fits folder
2025-12-17 09:00:49.700631 INFO::Writing residuals to file /tmp/RtmpW5dEye/file63a664c793/fits/residuals_linear.rds
2025-12-17 09:00:49.706688 INFO::Writing fitted values to file /tmp/RtmpW5dEye/file63a664c793/fits/fitted_linear.rds
2025-12-17 09:00:49.709748 INFO::Writing residuals to file /tmp/RtmpW5dEye/file63a664c793/fits/residuals_logistic.rds
2025-12-17 09:00:49.711902 INFO::Writing fitted values to file /tmp/RtmpW5dEye/file63a664c793/fits/fitted_logistic.rds
2025-12-17 09:00:49.716033 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpW5dEye/file63a664c793/all_results.tsv
2025-12-17 09:00:49.721598 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/RtmpW5dEye/file63a664c793/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
459.923 10.024 661.939
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 27.789 | 1.065 | 39.784 | |
| maaslin_check_arguments | 0.194 | 0.004 | 0.264 | |
| maaslin_check_formula | 0.195 | 0.010 | 0.290 | |
| maaslin_compute_formula | 0.198 | 0.011 | 0.305 | |
| maaslin_contrast_test | 22.712 | 1.336 | 33.265 | |
| maaslin_filter | 0.689 | 0.056 | 1.095 | |
| maaslin_fit | 15.483 | 0.582 | 21.897 | |
| maaslin_log_arguments | 0.195 | 0.009 | 0.253 | |
| maaslin_normalize | 0.450 | 0.032 | 0.655 | |
| maaslin_plot_results | 54.528 | 1.564 | 77.956 | |
| maaslin_plot_results_from_output | 55.171 | 1.309 | 78.857 | |
| maaslin_process_metadata | 0.737 | 0.053 | 1.023 | |
| maaslin_read_data | 0.185 | 0.009 | 0.260 | |
| maaslin_reorder_data | 0.192 | 0.009 | 0.240 | |
| maaslin_transform | 0.868 | 0.075 | 1.419 | |
| maaslin_write_results | 18.838 | 1.082 | 27.098 | |
| maaslin_write_results_lefse_format | 17.501 | 0.891 | 26.173 | |
| preprocess_dna_mtx | 0.004 | 0.000 | 0.012 | |
| preprocess_taxa_mtx | 0.004 | 0.001 | 0.005 | |