William Nickols
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9669f95 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:05 -0500 (Thu, 20 Nov 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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: 2025-11-18 09:40:41 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 10:09:08 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 1707.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maaslin3.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maaslin3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maaslin3_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* 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 101.305 1.400 113.144
maaslin_plot_results_from_output 100.598 1.533 105.972
maaslin_contrast_test 42.634 2.037 51.472
maaslin3 40.839 1.570 48.303
maaslin_write_results_lefse_format 36.604 0.515 39.082
maaslin_write_results 32.654 0.944 34.483
maaslin_fit 31.863 1.194 36.630
* 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 Patched (2025-11-05 r88990) -- "[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")
2025-11-18 09:55:00.671966 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:55:01.661084 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:55:01.907852 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:55:01.971854 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:55:02.084857 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:55:02.438105 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:55:02.457218 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:55:02.494855 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:55:02.767909 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:55:02.785804 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:55:02.994217 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:55:03.137748 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:55:03.190474 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:55:03.331262 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:55:03.534224 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:55:37.842335 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:55:38.062443 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:55:38.289011 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:55:38.351041 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:55:38.450001 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:55:38.68267 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:55:38.697965 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:55:38.734554 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:55:39.076716 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:55:39.091608 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:55:39.227509 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:55:39.345113 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:55:39.382046 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:55:39.504645 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:55:39.704105 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:55:49.472 R[70081:27627637] XType: com.apple.fonts is not accessible.
2025-11-18 09:55:49.472 R[70081:27627637] XType: XTFontStaticRegistry is enabled.
2025-11-18 09:56:37.331851 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:56:37.539142 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:56:37.7471 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:56:37.805699 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:56:37.903457 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:56:38.12471 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:56:38.139869 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:56:38.173406 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:56:38.46062 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:56:38.475706 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:56:38.627476 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:56:38.74664 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:56:38.783104 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:56:38.902883 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:56:39.120455 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:57:10.592827 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:57:10.802131 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:57:11.022583 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:57:11.086633 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:57:11.18912 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:57:11.403103 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:57:11.419178 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:57:11.451842 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:57:11.716626 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:57:11.730995 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:57:11.868787 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:57:11.988133 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:57:12.022008 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:57:12.139283 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:57:12.339021 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:57:12.895976 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/residuals_linear.rds
2025-11-18 09:57:13.004073 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/fitted_linear.rds
2025-11-18 09:57:13.124542 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/residuals_logistic.rds
2025-11-18 09:57:13.727658 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/fitted_logistic.rds
2025-11-18 09:58:04.7824 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:58:04.996268 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:58:05.214448 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:58:05.276072 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:58:05.37258 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:58:05.582227 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:58:05.597174 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:58:05.631267 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:58:05.889247 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:58:05.904934 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:58:06.045864 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:58:06.160138 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:58:06.193034 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:58:06.310056 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:58:06.51284 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:58:36.168236 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:58:36.379302 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:58:36.651138 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:58:36.710049 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:58:36.803105 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:58:37.00264 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:58:37.016286 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:58:37.047443 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:58:37.311192 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:58:37.326472 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:58:37.463023 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:58:37.568394 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:58:37.600505 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:58:37.713821 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:58:37.906561 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:58:38.427803 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/residuals_linear.rds
2025-11-18 09:58:38.535401 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/fitted_linear.rds
2025-11-18 09:58:38.64494 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/residuals_logistic.rds
2025-11-18 09:58:39.207998 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/fitted_logistic.rds
2025-11-18 09:59:28.392898 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:59:28.603706 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:59:28.793441 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:59:28.850484 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:59:28.942371 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:59:29.143505 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:59:29.157358 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:59:29.187731 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 09:59:29.450055 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 09:59:29.464009 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 09:59:29.607086 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 09:59:29.720604 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 09:59:29.751917 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 09:59:29.867179 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 09:59:30.075613 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 09:59:59.133254 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 09:59:59.342168 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 09:59:59.549596 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 09:59:59.609665 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 09:59:59.704752 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 09:59:59.911142 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 09:59:59.925108 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 09:59:59.957113 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 10:00:00.219059 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 10:00:00.236094 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 10:00:00.378552 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 10:00:00.483853 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 10:00:00.514424 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 10:00:00.623523 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 10:00:00.808132 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 10:00:01.438298 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/residuals_linear.rds
2025-11-18 10:00:01.548582 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/fitted_linear.rds
2025-11-18 10:00:01.668885 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/residuals_logistic.rds
2025-11-18 10:00:02.25055 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c1666a59c5/fits/fitted_logistic.rds
2025-11-18 10:00:51.671988 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 10:00:51.87559 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 10:00:52.088544 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 10:00:52.146497 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 10:00:52.241579 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 10:00:52.448812 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 10:00:52.463442 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 10:00:52.49329 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 10:00:52.765835 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 10:00:52.779454 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 10:00:52.917183 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 10:00:53.037681 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 10:00:53.073662 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 10:00:53.18945 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 10:00:53.413871 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 10:01:22.001154 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 10:01:22.210016 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 10:01:22.415346 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 10:01:22.474949 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 10:01:22.568469 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 10:01:22.773996 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 10:01:22.789826 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 10:01:22.821221 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 10:01:23.074406 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 10:01:23.088554 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 10:01:23.22263 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 10:01:23.335725 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 10:01:23.367289 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 10:01:23.474072 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 10:01:23.659754 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 10:02:18.829756 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:02:38.990449 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:03:35.733778 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:03:55.974597 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:03:57.628724 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_linear.rds
2025-11-18 10:03:57.732163 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_linear.rds
2025-11-18 10:03:57.798414 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_logistic.rds
2025-11-18 10:03:57.933075 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_logistic.rds
2025-11-18 10:04:50.2534 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:05:02.715383 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:05:03.47144 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_linear.rds
2025-11-18 10:05:03.575857 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_linear.rds
2025-11-18 10:05:03.645567 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_logistic.rds
2025-11-18 10:05:03.778109 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_logistic.rds
2025-11-18 10:05:47.775013 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:06:00.819066 WARNING::Fitting problem for feature 124 returning NA
2025-11-18 10:06:01.651988 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_linear.rds
2025-11-18 10:06:01.764197 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_linear.rds
2025-11-18 10:06:01.834552 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_logistic.rds
2025-11-18 10:06:01.976247 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_logistic.rds
2025-11-18 10:06:48.198477 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 10:06:48.440202 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 10:06:48.676644 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 10:06:48.74684 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 10:06:48.859242 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 10:06:49.103198 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 10:06:49.122891 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 10:06:49.158508 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 10:06:49.473341 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 10:06:49.490632 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 10:06:49.639284 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 10:06:49.757288 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 10:06:49.793805 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 10:06:49.908737 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 10:06:50.154464 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 10:07:21.014688 WARNING::Fitting problem for feature 50 returning NA
2025-11-18 10:07:21.231622 WARNING::Fitting problem for feature 62 returning NA
2025-11-18 10:07:21.442114 WARNING::Fitting problem for feature 74 returning NA
2025-11-18 10:07:21.502406 WARNING::Fitting problem for feature 78 returning NA
2025-11-18 10:07:21.595606 WARNING::Fitting problem for feature 84 returning NA
2025-11-18 10:07:21.807933 WARNING::Fitting problem for feature 96 returning NA
2025-11-18 10:07:21.821925 WARNING::Fitting problem for feature 97 returning NA
2025-11-18 10:07:21.858052 WARNING::Fitting problem for feature 99 returning NA
2025-11-18 10:07:22.113624 WARNING::Fitting problem for feature 114 returning NA
2025-11-18 10:07:22.129142 WARNING::Fitting problem for feature 115 returning NA
2025-11-18 10:07:22.263931 WARNING::Fitting problem for feature 123 returning NA
2025-11-18 10:07:22.374243 WARNING::Fitting problem for feature 130 returning NA
2025-11-18 10:07:22.405222 WARNING::Fitting problem for feature 132 returning NA
2025-11-18 10:07:22.518916 WARNING::Fitting problem for feature 139 returning NA
2025-11-18 10:07:22.701251 WARNING::Fitting problem for feature 150 returning NA
2025-11-18 10:07:23.372216 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_linear.rds
2025-11-18 10:07:23.479227 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_linear.rds
2025-11-18 10:07:23.591056 WARNING::Deleting existing residuals file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/residuals_logistic.rds
2025-11-18 10:07:24.180921 WARNING::Deleting existing fitted file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c14b3172df/fits/fitted_logistic.rds
2025-11-18 10:08:14.926569 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-11-18 10:08:14.975871 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-11-18 10:08:15.009971 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-11-18 10:08:15.166538 ERROR::No fixed, group, or
ordered effects included in formula.
2025-11-18 10:08:15.2155 ERROR::Effect name not found in metadata: d
2025-11-18 10:08:15.250452 ERROR::No user formula provided
2025-11-18 10:08:15.344645 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-11-18 10:08:15.380975 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-11-18 10:08:27.36505 INFO::Writing function arguments to log file
2025-11-18 10:08:27.409019 INFO::Verifying options selected are valid
2025-11-18 10:08:33.178251 INFO::Writing function arguments to log file
2025-11-18 10:08:33.213089 INFO::Verifying options selected are valid
2025-11-18 10:08:33.215854 INFO::Determining format of input files
2025-11-18 10:08:33.21854 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 10:08:33.224307 INFO::Running selected normalization method: TSS
2025-11-18 10:08:33.227928 INFO::Creating output feature tables folder
2025-11-18 10:08:33.230839 INFO::Writing normalized data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/features/data_norm.tsv
2025-11-18 10:08:33.235117 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-11-18 10:08:33.237895 INFO::Total samples in data: 16
2025-11-18 10:08:33.240486 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-11-18 10:08:33.243552 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-11-18 10:08:33.249543 INFO::Total filtered features: 0
2025-11-18 10:08:33.252502 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-11-18 10:08:33.255599 INFO::Total features filtered by non-zero variance filtering: 0
2025-11-18 10:08:33.258319 INFO::Filtered feature names from variance filtering:
2025-11-18 10:08:33.260936 INFO::Writing filtered data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/features/filtered_data.tsv
2025-11-18 10:08:33.265695 INFO::Running selected transform method: LOG
2025-11-18 10:08:33.269061 INFO::Writing normalized, filtered, transformed data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/features/data_transformed.tsv
2025-11-18 10:08:33.274221 INFO::Applying z-score to standardize continuous metadata
2025-11-18 10:08:33.285426 INFO::Running the linear model component
2025-11-18 10:08:33.329466 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:33.341648 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:33.353838 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:33.374169 INFO::Counting total values for each feature
2025-11-18 10:08:33.379184 INFO::Running the logistic model component
2025-11-18 10:08:33.422648 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:33.439406 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:33.455755 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:33.481848 INFO::Counting total values for each feature
2025-11-18 10:08:33.48764 INFO::Re-running abundances for warn_prevalence
2025-11-18 10:08:33.490726 INFO::Running selected normalization method: TSS
2025-11-18 10:08:33.494911 INFO::Running selected transform method: LOG
2025-11-18 10:08:33.537715 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:33.549564 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:33.560878 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:33.782141 INFO::Creating fits folder
2025-11-18 10:08:33.785539 INFO::Writing residuals to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/fits/residuals_linear.rds
2025-11-18 10:08:33.788736 INFO::Writing fitted values to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/fits/fitted_linear.rds
2025-11-18 10:08:33.792189 INFO::Writing residuals to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/fits/residuals_logistic.rds
2025-11-18 10:08:33.795549 INFO::Writing fitted values to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/fits/fitted_logistic.rds
2025-11-18 10:08:33.80259 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/all_results.tsv
2025-11-18 10:08:33.80775 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): /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/significant_results.tsv
2025-11-18 10:08:33.812107 INFO::Creating output figures folder
2025-11-18 10:08:33.816369 INFO::Writing summary plot of significant
results to file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/figures/summary_plot.pdf
2025-11-18 10:08:37.758851 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/figures
2025-11-18 10:08:37.763315 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 10:08:37.777503 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 10:08:39.054459 INFO::Writing summary plot of
significant results to file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/figures/summary_plot.pdf
2025-11-18 10:08:42.976758 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c168c9162e/figures
2025-11-18 10:08:42.980137 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 10:08:42.992608 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 10:08:44.280985 INFO::Running the linear model component
2025-11-18 10:08:44.30578 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:44.31708 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:44.329284 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:44.34746 INFO::Counting total values for each feature
2025-11-18 10:08:44.351499 INFO::Running the logistic model component
2025-11-18 10:08:44.374822 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:44.391328 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:44.407153 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:44.43127 INFO::Counting total values for each feature
2025-11-18 10:08:44.437085 INFO::Re-running abundances for warn_prevalence
2025-11-18 10:08:44.439108 INFO::Running selected normalization method: TSS
2025-11-18 10:08:44.442519 INFO::Running selected transform method: LOG
2025-11-18 10:08:44.466313 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:44.477738 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:44.49254 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:44.713638 INFO::Creating output folder
2025-11-18 10:08:44.715687 INFO::Creating output figures folder
2025-11-18 10:08:44.718635 INFO::Writing summary plot of significant
results to file: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c15769e29e/figures/summary_plot.pdf
2025-11-18 10:08:48.742265 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c15769e29e/figures
2025-11-18 10:08:48.745699 INFO::Plotting associations from most to least significant, grouped by metadata
2025-11-18 10:08:48.758828 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-11-18 10:08:51.584115 INFO::Applying z-score to standardize continuous metadata
2025-11-18 10:08:51.602526 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-11-18 10:08:51.604439 INFO::Bypass z-score application to metadata
2025-11-18 10:08:51.610032 INFO::Bypass z-score application to metadata
2025-11-18 10:08:51.666077 INFO::Determining format of input files
2025-11-18 10:08:51.668214 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 10:08:51.672791 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-11-18 10:08:51.695662 INFO::Determining format of input files
2025-11-18 10:08:51.698799 INFO::Input format is data samples as columns and metadata samples as rows
2025-11-18 10:08:51.702381 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 10:08:51.723864 INFO::Determining format of input files
2025-11-18 10:08:51.726067 INFO::Input format is data samples as rows and metadata samples as rows
2025-11-18 10:08:51.729063 INFO::Input format is feature_specific_covariate samples as columns
2025-11-18 10:08:51.733159 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-11-18 10:08:51.735357 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-11-18 10:08:51.769785 INFO::Running selected transform method: LOG
2025-11-18 10:08:51.772488 INFO::Creating output feature tables folder
2025-11-18 10:08:51.775377 INFO::Writing normalized, filtered, transformed data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c13e021951/features/data_transformed.tsv
2025-11-18 10:08:51.785997 INFO::Running selected transform method: LOG
2025-11-18 10:08:51.788538 INFO::Writing normalized, filtered, transformed data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c13e021951/features/data_transformed.tsv
2025-11-18 10:08:51.798697 INFO::Running selected transform method: PLOG
2025-11-18 10:08:51.804612 INFO::Writing normalized, filtered, transformed data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c13e021951/features/data_transformed.tsv
2025-11-18 10:08:51.811657 INFO::Running selected transform method: NONE
2025-11-18 10:08:51.813478 INFO::Writing normalized, filtered, transformed data to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c13e021951/features/data_transformed.tsv
2025-11-18 10:08:51.833815 INFO::Running the linear model component
2025-11-18 10:08:51.856883 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:51.869256 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:51.88134 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:51.90269 INFO::Counting total values for each feature
2025-11-18 10:08:51.908704 INFO::Running the logistic model component
2025-11-18 10:08:51.936095 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:51.951866 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:51.970964 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:51.996507 INFO::Counting total values for each feature
2025-11-18 10:08:52.001944 INFO::Re-running abundances for warn_prevalence
2025-11-18 10:08:52.004003 INFO::Running selected normalization method: TSS
2025-11-18 10:08:52.007295 INFO::Running selected transform method: LOG
2025-11-18 10:08:52.032082 INFO::Fitting model to feature number 1, a
2025-11-18 10:08:52.042753 INFO::Fitting model to feature number 2, b
2025-11-18 10:08:52.055735 INFO::Fitting model to feature number 3, c
2025-11-18 10:08:52.303396 INFO::Creating output folder
2025-11-18 10:08:52.306208 INFO::Creating fits folder
2025-11-18 10:08:52.308807 INFO::Writing residuals to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c17bcc34a4/fits/residuals_linear.rds
2025-11-18 10:08:52.314362 INFO::Writing fitted values to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c17bcc34a4/fits/fitted_linear.rds
2025-11-18 10:08:52.317245 INFO::Writing residuals to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c17bcc34a4/fits/residuals_logistic.rds
2025-11-18 10:08:52.320019 INFO::Writing fitted values to file /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c17bcc34a4/fits/fitted_logistic.rds
2025-11-18 10:08:52.327768 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c17bcc34a4/all_results.tsv
2025-11-18 10:08:52.3334 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): /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T//RtmplbfvBo/file111c17bcc34a4/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
805.521 13.111 855.507
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 40.839 | 1.570 | 48.303 | |
| maaslin_check_arguments | 0.282 | 0.007 | 0.314 | |
| maaslin_check_formula | 0.298 | 0.016 | 0.339 | |
| maaslin_compute_formula | 0.309 | 0.018 | 0.364 | |
| maaslin_contrast_test | 42.634 | 2.037 | 51.472 | |
| maaslin_filter | 1.197 | 0.084 | 1.428 | |
| maaslin_fit | 31.863 | 1.194 | 36.630 | |
| maaslin_log_arguments | 0.280 | 0.014 | 0.315 | |
| maaslin_normalize | 0.665 | 0.041 | 0.753 | |
| maaslin_plot_results | 101.305 | 1.400 | 113.144 | |
| maaslin_plot_results_from_output | 100.598 | 1.533 | 105.972 | |
| maaslin_process_metadata | 1.210 | 0.079 | 1.351 | |
| maaslin_read_data | 0.280 | 0.015 | 0.327 | |
| maaslin_reorder_data | 0.292 | 0.015 | 0.328 | |
| maaslin_transform | 1.548 | 0.120 | 1.769 | |
| maaslin_write_results | 32.654 | 0.944 | 34.483 | |
| maaslin_write_results_lefse_format | 36.604 | 0.515 | 39.082 | |
| preprocess_dna_mtx | 0.008 | 0.001 | 0.010 | |
| preprocess_taxa_mtx | 0.010 | 0.001 | 0.011 | |