William Nickols
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 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 2025-12-11 12:05 -0500 (Thu, 11 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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: 2025-12-09 07:13:07 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 07:42:25 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 1757.5 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 102.282 1.620 113.573
maaslin_plot_results_from_output 100.971 1.484 110.908
maaslin_contrast_test 42.597 1.764 49.447
maaslin3 41.958 1.572 49.462
maaslin_write_results_lefse_format 38.088 0.922 46.450
maaslin_write_results 31.823 0.952 34.672
maaslin_fit 30.498 1.069 35.208
* 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")
2025-12-09 07:27:46.682987 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:27:47.66184 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:27:48.020199 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:27:48.086292 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:27:48.187216 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:27:48.410809 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:27:48.434059 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:27:48.49511 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:27:48.838116 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:27:48.852072 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:27:48.989196 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:27:49.101142 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:27:49.138531 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:27:49.271448 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:27:49.469694 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:28:24.155568 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:28:24.367911 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:28:24.576781 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:28:24.641241 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:28:24.738913 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:28:24.98998 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:28:25.004609 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:28:25.038928 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:28:25.311826 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:28:25.326702 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:28:25.475617 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:28:25.589992 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:28:25.623791 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:28:25.738791 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:28:25.929264 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:28:35.686 R[64648:106160767] XType: com.apple.fonts is not accessible.
2025-12-09 07:28:35.686 R[64648:106160767] XType: XTFontStaticRegistry is enabled.
2025-12-09 07:29:25.357873 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:29:25.640348 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:29:25.879711 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:29:25.940803 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:29:26.037064 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:29:26.253631 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:29:26.26762 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:29:26.300101 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:29:26.572566 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:29:26.587125 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:29:26.72975 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:29:26.863757 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:29:26.901528 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:29:27.016077 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:29:27.21607 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:29:58.1128 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:29:58.372579 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:29:58.641176 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:29:58.704298 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:29:58.802315 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:29:59.019859 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:29:59.033884 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:29:59.066404 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:29:59.387853 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:29:59.403857 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:29:59.554065 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:29:59.682787 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:29:59.724462 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:29:59.885438 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:30:00.096503 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:30:00.698388 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/residuals_linear.rds
2025-12-09 07:30:00.796441 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/fitted_linear.rds
2025-12-09 07:30:00.902717 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/residuals_logistic.rds
2025-12-09 07:30:01.502635 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/fitted_logistic.rds
2025-12-09 07:30:54.686101 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:30:54.892296 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:30:55.101209 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:30:55.168467 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:30:55.272843 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:30:55.47801 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:30:55.491392 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:30:55.523934 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:30:55.799734 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:30:55.814874 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:30:55.95756 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:30:56.079747 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:30:56.113736 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:30:56.234778 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:30:56.439109 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:31:25.855315 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:31:26.06933 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:31:26.289794 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:31:26.360436 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:31:26.45893 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:31:26.673394 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:31:26.687842 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:31:26.721791 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:31:26.991407 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:31:27.006428 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:31:27.156341 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:31:27.269834 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:31:27.302994 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:31:27.417561 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:31:27.616429 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:31:28.23335 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/residuals_linear.rds
2025-12-09 07:31:28.345905 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/fitted_linear.rds
2025-12-09 07:31:28.45882 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/residuals_logistic.rds
2025-12-09 07:31:29.088727 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/fitted_logistic.rds
2025-12-09 07:32:20.587223 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:32:20.789439 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:32:20.991199 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:32:21.05462 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:32:21.154734 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:32:21.391514 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:32:21.404451 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:32:21.439449 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:32:21.722941 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:32:21.740862 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:32:21.914707 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:32:22.04422 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:32:22.080424 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:32:22.213429 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:32:22.469932 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:32:52.186977 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:32:52.416186 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:32:52.629395 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:32:52.693343 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:32:52.788048 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:32:53.004743 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:32:53.02168 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:32:53.055043 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:32:53.368026 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:32:53.383859 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:32:53.528393 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:32:53.646346 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:32:53.681455 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:32:53.793772 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:32:54.063084 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:32:54.61476 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/residuals_linear.rds
2025-12-09 07:32:54.737225 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/fitted_linear.rds
2025-12-09 07:32:54.858883 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/residuals_logistic.rds
2025-12-09 07:32:55.597585 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc8852971ea1/fits/fitted_logistic.rds
2025-12-09 07:33:47.980218 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:33:48.203251 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:33:48.426171 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:33:48.491281 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:33:48.592927 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:33:48.812483 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:33:48.826942 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:33:48.860337 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:33:49.142121 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:33:49.157142 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:33:49.297389 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:33:49.414067 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:33:49.445354 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:33:49.566973 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:33:49.767503 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:34:18.022657 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:34:18.275645 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:34:18.51164 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:34:18.579696 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:34:18.695056 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:34:19.033857 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:34:19.050695 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:34:19.088618 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:34:19.388658 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:34:19.402932 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:34:19.54871 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:34:19.663164 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:34:19.698222 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:34:19.812934 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:34:20.021053 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:35:17.89783 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:35:38.668901 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:36:37.828028 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:36:57.243869 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:36:58.947914 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_linear.rds
2025-12-09 07:36:59.06199 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_linear.rds
2025-12-09 07:36:59.133753 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_logistic.rds
2025-12-09 07:36:59.283655 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_logistic.rds
2025-12-09 07:37:55.69482 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:38:07.452804 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:38:08.28632 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_linear.rds
2025-12-09 07:38:08.396422 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_linear.rds
2025-12-09 07:38:08.465886 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_logistic.rds
2025-12-09 07:38:08.611016 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_logistic.rds
2025-12-09 07:38:55.753554 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:39:08.973109 WARNING::Fitting problem for feature 124 returning NA
2025-12-09 07:39:09.861352 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_linear.rds
2025-12-09 07:39:09.976389 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_linear.rds
2025-12-09 07:39:10.054122 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_logistic.rds
2025-12-09 07:39:10.203936 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_logistic.rds
2025-12-09 07:40:00.711805 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:40:00.97179 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:40:01.226881 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:40:01.299421 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:40:01.41902 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:40:01.670147 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:40:01.690196 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:40:01.729369 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:40:02.050707 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:40:02.066866 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:40:02.229825 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:40:02.366595 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:40:02.407529 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:40:02.533792 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:40:02.797503 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:40:32.503031 WARNING::Fitting problem for feature 50 returning NA
2025-12-09 07:40:32.731996 WARNING::Fitting problem for feature 62 returning NA
2025-12-09 07:40:32.994597 WARNING::Fitting problem for feature 74 returning NA
2025-12-09 07:40:33.066157 WARNING::Fitting problem for feature 78 returning NA
2025-12-09 07:40:33.180057 WARNING::Fitting problem for feature 84 returning NA
2025-12-09 07:40:33.431295 WARNING::Fitting problem for feature 96 returning NA
2025-12-09 07:40:33.448918 WARNING::Fitting problem for feature 97 returning NA
2025-12-09 07:40:33.483212 WARNING::Fitting problem for feature 99 returning NA
2025-12-09 07:40:33.909057 WARNING::Fitting problem for feature 114 returning NA
2025-12-09 07:40:33.925415 WARNING::Fitting problem for feature 115 returning NA
2025-12-09 07:40:34.093216 WARNING::Fitting problem for feature 123 returning NA
2025-12-09 07:40:34.228043 WARNING::Fitting problem for feature 130 returning NA
2025-12-09 07:40:34.267479 WARNING::Fitting problem for feature 132 returning NA
2025-12-09 07:40:34.400975 WARNING::Fitting problem for feature 139 returning NA
2025-12-09 07:40:34.635165 WARNING::Fitting problem for feature 150 returning NA
2025-12-09 07:40:35.406395 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_linear.rds
2025-12-09 07:40:35.53294 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_linear.rds
2025-12-09 07:40:35.656483 WARNING::Deleting existing residuals file: /tmp/RtmpJav3Fy/filefc886586d159/fits/residuals_logistic.rds
2025-12-09 07:40:36.348576 WARNING::Deleting existing fitted file: /tmp/RtmpJav3Fy/filefc886586d159/fits/fitted_logistic.rds
2025-12-09 07:41:29.665446 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-09 07:41:29.717388 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-09 07:41:29.756337 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-09 07:41:29.903375 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-09 07:41:29.94925 ERROR::Effect name not found in metadata: d
2025-12-09 07:41:29.981878 ERROR::No user formula provided
2025-12-09 07:41:30.071996 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-09 07:41:30.110037 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-09 07:41:41.223064 INFO::Writing function arguments to log file
2025-12-09 07:41:41.27773 INFO::Verifying options selected are valid
2025-12-09 07:41:47.94552 INFO::Writing function arguments to log file
2025-12-09 07:41:48.007769 INFO::Verifying options selected are valid
2025-12-09 07:41:48.012108 INFO::Determining format of input files
2025-12-09 07:41:48.021399 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-09 07:41:48.027183 INFO::Running selected normalization method: TSS
2025-12-09 07:41:48.035382 INFO::Creating output feature tables folder
2025-12-09 07:41:48.038252 INFO::Writing normalized data to file /tmp/RtmpJav3Fy/filefc88352a9961/features/data_norm.tsv
2025-12-09 07:41:48.04235 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-09 07:41:48.046549 INFO::Total samples in data: 16
2025-12-09 07:41:48.049843 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-09 07:41:48.054113 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-09 07:41:48.059557 INFO::Total filtered features: 0
2025-12-09 07:41:48.062238 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-09 07:41:48.072093 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-09 07:41:48.076328 INFO::Filtered feature names from variance filtering:
2025-12-09 07:41:48.079389 INFO::Writing filtered data to file /tmp/RtmpJav3Fy/filefc88352a9961/features/filtered_data.tsv
2025-12-09 07:41:48.086056 INFO::Running selected transform method: LOG
2025-12-09 07:41:48.089673 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpJav3Fy/filefc88352a9961/features/data_transformed.tsv
2025-12-09 07:41:48.094831 INFO::Applying z-score to standardize continuous metadata
2025-12-09 07:41:48.109346 INFO::Running the linear model component
2025-12-09 07:41:48.160169 INFO::Fitting model to feature number 1, a
2025-12-09 07:41:48.172976 INFO::Fitting model to feature number 2, b
2025-12-09 07:41:48.187281 INFO::Fitting model to feature number 3, c
2025-12-09 07:41:48.206998 INFO::Counting total values for each feature
2025-12-09 07:41:48.211989 INFO::Running the logistic model component
2025-12-09 07:41:48.259256 INFO::Fitting model to feature number 1, a
2025-12-09 07:41:48.279802 INFO::Fitting model to feature number 2, b
2025-12-09 07:41:48.297466 INFO::Fitting model to feature number 3, c
2025-12-09 07:41:48.324611 INFO::Counting total values for each feature
2025-12-09 07:41:48.330502 INFO::Re-running abundances for warn_prevalence
2025-12-09 07:41:48.334696 INFO::Running selected normalization method: TSS
2025-12-09 07:41:48.338918 INFO::Running selected transform method: LOG
2025-12-09 07:41:48.383372 INFO::Fitting model to feature number 1, a
2025-12-09 07:41:48.398523 INFO::Fitting model to feature number 2, b
2025-12-09 07:41:48.414503 INFO::Fitting model to feature number 3, c
2025-12-09 07:41:48.672392 INFO::Creating fits folder
2025-12-09 07:41:48.67537 INFO::Writing residuals to file /tmp/RtmpJav3Fy/filefc88352a9961/fits/residuals_linear.rds
2025-12-09 07:41:48.680178 INFO::Writing fitted values to file /tmp/RtmpJav3Fy/filefc88352a9961/fits/fitted_linear.rds
2025-12-09 07:41:48.683709 INFO::Writing residuals to file /tmp/RtmpJav3Fy/filefc88352a9961/fits/residuals_logistic.rds
2025-12-09 07:41:48.68739 INFO::Writing fitted values to file /tmp/RtmpJav3Fy/filefc88352a9961/fits/fitted_logistic.rds
2025-12-09 07:41:48.697195 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpJav3Fy/filefc88352a9961/all_results.tsv
2025-12-09 07:41:48.705672 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/RtmpJav3Fy/filefc88352a9961/significant_results.tsv
2025-12-09 07:41:48.710184 INFO::Creating output figures folder
2025-12-09 07:41:48.715345 INFO::Writing summary plot of significant
results to file: /tmp/RtmpJav3Fy/filefc88352a9961/figures/summary_plot.pdf
2025-12-09 07:41:53.02127 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpJav3Fy/filefc88352a9961/figures
2025-12-09 07:41:53.025224 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-09 07:41:53.038619 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-09 07:41:54.316115 INFO::Writing summary plot of
significant results to file: /tmp/RtmpJav3Fy/filefc88352a9961/figures/summary_plot.pdf
2025-12-09 07:41:58.688407 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpJav3Fy/filefc88352a9961/figures
2025-12-09 07:41:58.691958 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-09 07:41:58.703578 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-09 07:41:59.956939 INFO::Running the linear model component
2025-12-09 07:41:59.980744 INFO::Fitting model to feature number 1, a
2025-12-09 07:41:59.991737 INFO::Fitting model to feature number 2, b
2025-12-09 07:42:00.00231 INFO::Fitting model to feature number 3, c
2025-12-09 07:42:00.020155 INFO::Counting total values for each feature
2025-12-09 07:42:00.024174 INFO::Running the logistic model component
2025-12-09 07:42:00.046512 INFO::Fitting model to feature number 1, a
2025-12-09 07:42:00.064951 INFO::Fitting model to feature number 2, b
2025-12-09 07:42:00.081501 INFO::Fitting model to feature number 3, c
2025-12-09 07:42:00.104416 INFO::Counting total values for each feature
2025-12-09 07:42:00.109717 INFO::Re-running abundances for warn_prevalence
2025-12-09 07:42:00.111862 INFO::Running selected normalization method: TSS
2025-12-09 07:42:00.115437 INFO::Running selected transform method: LOG
2025-12-09 07:42:00.140972 INFO::Fitting model to feature number 1, a
2025-12-09 07:42:00.152356 INFO::Fitting model to feature number 2, b
2025-12-09 07:42:00.162354 INFO::Fitting model to feature number 3, c
2025-12-09 07:42:00.382778 INFO::Creating output folder
2025-12-09 07:42:00.385196 INFO::Creating output figures folder
2025-12-09 07:42:00.388768 INFO::Writing summary plot of significant
results to file: /tmp/RtmpJav3Fy/filefc885cac6cf4/figures/summary_plot.pdf
2025-12-09 07:42:05.14418 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmpJav3Fy/filefc885cac6cf4/figures
2025-12-09 07:42:05.147574 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-09 07:42:05.160535 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-09 07:42:08.040879 INFO::Applying z-score to standardize continuous metadata
2025-12-09 07:42:08.061828 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-09 07:42:08.06566 INFO::Bypass z-score application to metadata
2025-12-09 07:42:08.072496 INFO::Bypass z-score application to metadata
2025-12-09 07:42:08.129474 INFO::Determining format of input files
2025-12-09 07:42:08.131481 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-09 07:42:08.134532 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-09 07:42:08.155997 INFO::Determining format of input files
2025-12-09 07:42:08.15937 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-09 07:42:08.162526 INFO::Input format is feature_specific_covariate samples as columns
2025-12-09 07:42:08.188095 INFO::Determining format of input files
2025-12-09 07:42:08.190459 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-09 07:42:08.19372 INFO::Input format is feature_specific_covariate samples as columns
2025-12-09 07:42:08.197854 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-09 07:42:08.199834 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-09 07:42:08.232878 INFO::Running selected transform method: LOG
2025-12-09 07:42:08.235295 INFO::Creating output feature tables folder
2025-12-09 07:42:08.239964 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpJav3Fy/filefc88fce9834/features/data_transformed.tsv
2025-12-09 07:42:08.253189 INFO::Running selected transform method: LOG
2025-12-09 07:42:08.255554 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpJav3Fy/filefc88fce9834/features/data_transformed.tsv
2025-12-09 07:42:08.266292 INFO::Running selected transform method: PLOG
2025-12-09 07:42:08.27029 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpJav3Fy/filefc88fce9834/features/data_transformed.tsv
2025-12-09 07:42:08.278874 INFO::Running selected transform method: NONE
2025-12-09 07:42:08.280883 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmpJav3Fy/filefc88fce9834/features/data_transformed.tsv
2025-12-09 07:42:08.303816 INFO::Running the linear model component
2025-12-09 07:42:08.330184 INFO::Fitting model to feature number 1, a
2025-12-09 07:42:08.342569 INFO::Fitting model to feature number 2, b
2025-12-09 07:42:08.354401 INFO::Fitting model to feature number 3, c
2025-12-09 07:42:08.37399 INFO::Counting total values for each feature
2025-12-09 07:42:08.377986 INFO::Running the logistic model component
2025-12-09 07:42:08.40101 INFO::Fitting model to feature number 1, a
2025-12-09 07:42:08.422239 INFO::Fitting model to feature number 2, b
2025-12-09 07:42:08.441079 INFO::Fitting model to feature number 3, c
2025-12-09 07:42:08.468668 INFO::Counting total values for each feature
2025-12-09 07:42:08.474981 INFO::Re-running abundances for warn_prevalence
2025-12-09 07:42:08.477058 INFO::Running selected normalization method: TSS
2025-12-09 07:42:08.481063 INFO::Running selected transform method: LOG
2025-12-09 07:42:08.50933 INFO::Fitting model to feature number 1, a
2025-12-09 07:42:08.523659 INFO::Fitting model to feature number 2, b
2025-12-09 07:42:08.535568 INFO::Fitting model to feature number 3, c
2025-12-09 07:42:08.78938 INFO::Creating output folder
2025-12-09 07:42:08.791702 INFO::Creating fits folder
2025-12-09 07:42:08.794825 INFO::Writing residuals to file /tmp/RtmpJav3Fy/filefc88446a8607/fits/residuals_linear.rds
2025-12-09 07:42:08.798411 INFO::Writing fitted values to file /tmp/RtmpJav3Fy/filefc88446a8607/fits/fitted_linear.rds
2025-12-09 07:42:08.801169 INFO::Writing residuals to file /tmp/RtmpJav3Fy/filefc88446a8607/fits/residuals_logistic.rds
2025-12-09 07:42:08.804034 INFO::Writing fitted values to file /tmp/RtmpJav3Fy/filefc88446a8607/fits/fitted_logistic.rds
2025-12-09 07:42:08.812312 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmpJav3Fy/filefc88446a8607/all_results.tsv
2025-12-09 07:42:08.816602 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/RtmpJav3Fy/filefc88446a8607/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
807.246 12.726 886.006
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 41.958 | 1.572 | 49.462 | |
| maaslin_check_arguments | 0.281 | 0.007 | 0.316 | |
| maaslin_check_formula | 0.295 | 0.014 | 0.380 | |
| maaslin_compute_formula | 0.302 | 0.016 | 0.373 | |
| maaslin_contrast_test | 42.597 | 1.764 | 49.447 | |
| maaslin_filter | 1.195 | 0.081 | 1.399 | |
| maaslin_fit | 30.498 | 1.069 | 35.208 | |
| maaslin_log_arguments | 0.290 | 0.014 | 0.347 | |
| maaslin_normalize | 0.681 | 0.044 | 0.836 | |
| maaslin_plot_results | 102.282 | 1.620 | 113.573 | |
| maaslin_plot_results_from_output | 100.971 | 1.484 | 110.908 | |
| maaslin_process_metadata | 1.225 | 0.078 | 1.383 | |
| maaslin_read_data | 0.277 | 0.014 | 0.301 | |
| maaslin_reorder_data | 0.296 | 0.015 | 0.326 | |
| maaslin_transform | 1.534 | 0.122 | 1.737 | |
| maaslin_write_results | 31.823 | 0.952 | 34.672 | |
| maaslin_write_results_lefse_format | 38.088 | 0.922 | 46.450 | |
| preprocess_dna_mtx | 0.008 | 0.001 | 0.009 | |
| preprocess_taxa_mtx | 0.010 | 0.001 | 0.013 | |