William Nickols
| Snapshot Date: 2025-09-01 13:45 -0400 (Mon, 01 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: ed6ae28 |
| git_last_commit_date: 2025-04-15 13:45:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-02 12:02 -0400 (Tue, 02 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1149/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.1.0 (landing page) William Nickols
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | NA | NA | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2025-09-01 21:45:53 -0400 (Mon, 01 Sep 2025) |
| EndedAt: 2025-09-01 21:58:39 -0400 (Mon, 01 Sep 2025) |
| EllapsedTime: 766.6 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maaslin3.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.1.0’
* 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 42.080 1.126 43.523
maaslin_plot_results 41.388 0.994 42.673
maaslin3 23.791 1.052 25.084
maaslin_contrast_test 19.390 0.965 20.512
maaslin_write_results_lefse_format 16.697 0.737 17.544
maaslin_write_results 15.256 0.860 16.218
maaslin_fit 13.896 0.763 14.754
* 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 ‘1.1.0’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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")
2025-09-01 21:52:42.9507 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:52:43.047504 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:52:43.154343 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:52:43.183437 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:52:43.243233 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:52:43.340274 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:52:43.348532 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:52:43.366179 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:52:43.502771 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:52:43.509226 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:52:43.565956 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:52:43.62263 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:52:43.639744 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:52:43.686782 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:52:43.785503 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:53:01.327141 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:53:01.438631 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:53:01.532125 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:53:01.560267 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:53:01.606051 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:53:01.702356 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:53:01.710342 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:53:01.726536 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:53:01.837078 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:53:01.846216 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:53:01.912223 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:53:01.961838 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:53:01.978205 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:53:02.024677 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:53:02.112234 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:53:05.739 R[33809:176387660] XType: com.apple.fonts is not accessible.
2025-09-01 21:53:05.739 R[33809:176387660] XType: XTFontStaticRegistry is enabled.
2025-09-01 21:53:22.606669 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:53:22.707765 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:53:22.841476 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:53:22.86729 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:53:22.913507 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:53:23.013108 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:53:23.020322 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:53:23.037108 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:53:23.159874 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:53:23.185172 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:53:23.254518 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:53:23.310544 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:53:23.329378 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:53:23.378012 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:53:23.520577 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:53:38.570221 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:53:38.662808 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:53:38.757839 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:53:38.786336 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:53:38.828639 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:53:38.921025 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:53:38.927382 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:53:38.940617 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:53:39.086342 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:53:39.094934 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:53:39.167168 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:53:39.221218 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:53:39.239709 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:53:39.294059 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:53:39.381014 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:53:39.664673 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file84114fc3164b/fits/residuals_linear.rds
2025-09-01 21:53:39.744506 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file84114fc3164b/fits/fitted_linear.rds
2025-09-01 21:53:39.821172 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file84114fc3164b/fits/residuals_logistic.rds
2025-09-01 21:53:40.173733 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file84114fc3164b/fits/fitted_logistic.rds
2025-09-01 21:53:59.08547 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:53:59.169687 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:53:59.265788 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:53:59.297098 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:53:59.343356 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:53:59.453269 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:53:59.460894 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:53:59.48014 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:53:59.612309 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:53:59.618595 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:53:59.688014 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:53:59.739767 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:53:59.752685 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:53:59.81419 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:53:59.906788 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:54:14.65023 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:54:14.751054 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:54:14.850927 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:54:14.881474 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:54:14.932613 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:54:15.03872 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:54:15.045847 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:54:15.059522 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:54:15.262721 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:54:15.271997 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:54:15.339151 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:54:15.396642 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:54:15.41177 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:54:15.462644 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:54:15.546643 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:54:15.782809 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file84114fc3164b/fits/residuals_linear.rds
2025-09-01 21:54:15.852049 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file84114fc3164b/fits/fitted_linear.rds
2025-09-01 21:54:15.921751 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file84114fc3164b/fits/residuals_logistic.rds
2025-09-01 21:54:16.264152 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file84114fc3164b/fits/fitted_logistic.rds
2025-09-01 21:54:34.903226 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:54:35.010931 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:54:35.114109 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:54:35.143239 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:54:35.189824 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:54:35.292702 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:54:35.298404 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:54:35.311145 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:54:35.424934 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:54:35.4324 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:54:35.498046 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:54:35.552091 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:54:35.56603 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:54:35.617506 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:54:35.711357 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:54:49.64295 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:54:49.731981 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:54:49.82277 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:54:49.85188 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:54:49.897465 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:54:49.985019 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:54:49.991666 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:54:50.006383 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:54:50.169004 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:54:50.174762 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:54:50.222388 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:54:50.269815 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:54:50.284278 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:54:50.327752 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:54:50.413383 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:54:50.641923 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file84114fc3164b/fits/residuals_linear.rds
2025-09-01 21:54:50.70222 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file84114fc3164b/fits/fitted_linear.rds
2025-09-01 21:54:50.765966 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file84114fc3164b/fits/residuals_logistic.rds
2025-09-01 21:54:51.111824 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file84114fc3164b/fits/fitted_logistic.rds
2025-09-01 21:55:09.814569 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:55:09.933939 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:55:10.044448 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:55:10.079972 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:55:10.137218 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:55:10.245064 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:55:10.252646 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:55:10.269796 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:55:10.389295 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:55:10.394949 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:55:10.459752 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:55:10.508707 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:55:10.524757 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:55:10.581892 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:55:10.68696 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:55:24.989796 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:55:25.089511 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:55:25.178806 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:55:25.205064 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:55:25.243489 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:55:25.325394 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:55:25.33097 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:55:25.34313 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:55:25.457924 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:55:25.464741 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:55:25.522786 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:55:25.572633 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:55:25.588177 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:55:25.638776 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:55:25.720602 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:55:47.060037 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:55:58.378275 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:56:21.057695 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:56:32.093074 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:56:32.827906 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_linear.rds
2025-09-01 21:56:32.890511 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_linear.rds
2025-09-01 21:56:32.932506 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_logistic.rds
2025-09-01 21:56:33.010947 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_logistic.rds
2025-09-01 21:56:53.306786 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:57:00.40265 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:57:00.766218 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_linear.rds
2025-09-01 21:57:00.831517 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_linear.rds
2025-09-01 21:57:00.867671 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_logistic.rds
2025-09-01 21:57:00.941933 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_logistic.rds
2025-09-01 21:57:17.227789 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:57:24.350595 WARNING::Fitting problem for feature 124 returning NA
2025-09-01 21:57:24.709634 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_linear.rds
2025-09-01 21:57:24.775345 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_linear.rds
2025-09-01 21:57:24.813938 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_logistic.rds
2025-09-01 21:57:24.882504 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_logistic.rds
2025-09-01 21:57:40.47778 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:57:40.571382 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:57:40.711887 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:57:40.741184 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:57:40.781865 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:57:40.87407 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:57:40.881955 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:57:40.896399 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:57:41.006285 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:57:41.013773 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:57:41.076163 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:57:41.128959 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:57:41.147578 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:57:41.207828 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:57:41.299071 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:57:54.780893 WARNING::Fitting problem for feature 50 returning NA
2025-09-01 21:57:54.880816 WARNING::Fitting problem for feature 62 returning NA
2025-09-01 21:57:54.970709 WARNING::Fitting problem for feature 74 returning NA
2025-09-01 21:57:54.997659 WARNING::Fitting problem for feature 78 returning NA
2025-09-01 21:57:55.04636 WARNING::Fitting problem for feature 84 returning NA
2025-09-01 21:57:55.157266 WARNING::Fitting problem for feature 96 returning NA
2025-09-01 21:57:55.163047 WARNING::Fitting problem for feature 97 returning NA
2025-09-01 21:57:55.180355 WARNING::Fitting problem for feature 99 returning NA
2025-09-01 21:57:55.29476 WARNING::Fitting problem for feature 114 returning NA
2025-09-01 21:57:55.300993 WARNING::Fitting problem for feature 115 returning NA
2025-09-01 21:57:55.370533 WARNING::Fitting problem for feature 123 returning NA
2025-09-01 21:57:55.418338 WARNING::Fitting problem for feature 130 returning NA
2025-09-01 21:57:55.430659 WARNING::Fitting problem for feature 132 returning NA
2025-09-01 21:57:55.478781 WARNING::Fitting problem for feature 139 returning NA
2025-09-01 21:57:55.56506 WARNING::Fitting problem for feature 150 returning NA
2025-09-01 21:57:55.914436 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_linear.rds
2025-09-01 21:57:55.984353 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_linear.rds
2025-09-01 21:57:56.047874 WARNING::Deleting existing residuals file: /tmp/RtmppHDurU/file8411383004f5/fits/residuals_logistic.rds
2025-09-01 21:57:56.397494 WARNING::Deleting existing fitted file: /tmp/RtmppHDurU/file8411383004f5/fits/fitted_logistic.rds
2025-09-01 21:58:14.297462 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-09-01 21:58:14.318245 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-09-01 21:58:14.33576 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-09-01 21:58:14.407647 ERROR::No fixed, group, or
ordered effects included in formula.
2025-09-01 21:58:14.432361 ERROR::Effect name not found in metadata: d
2025-09-01 21:58:14.446504 ERROR::No user formula provided
2025-09-01 21:58:14.493491 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-09-01 21:58:14.509459 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-09-01 21:58:17.886001 INFO::Writing function arguments to log file
2025-09-01 21:58:17.910471 INFO::Verifying options selected are valid
2025-09-01 21:58:20.065968 INFO::Writing function arguments to log file
2025-09-01 21:58:20.08462 INFO::Verifying options selected are valid
2025-09-01 21:58:20.085851 INFO::Determining format of input files
2025-09-01 21:58:20.087422 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-01 21:58:20.090264 INFO::Running selected normalization method: TSS
2025-09-01 21:58:20.091783 INFO::Creating output feature tables folder
2025-09-01 21:58:20.093086 INFO::Writing normalized data to file /tmp/RtmppHDurU/file84112e344a5c/features/data_norm.tsv
2025-09-01 21:58:20.09503 INFO::Filter data based on min abundance and min prevalence
2025-09-01 21:58:20.096574 INFO::Total samples in data: 16
2025-09-01 21:58:20.097663 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-09-01 21:58:20.100376 INFO::Total filtered features: 0
2025-09-01 21:58:20.101541 INFO::Filtered feature names from abundance and prevalence filtering:
2025-09-01 21:58:20.102789 INFO::Total features filtered by non-zero variance filtering: 0
2025-09-01 21:58:20.104479 INFO::Filtered feature names from variance filtering:
2025-09-01 21:58:20.105984 INFO::Writing filtered data to file /tmp/RtmppHDurU/file84112e344a5c/features/filtered_data.tsv
2025-09-01 21:58:20.108685 INFO::Running selected transform method: LOG
2025-09-01 21:58:20.110617 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmppHDurU/file84112e344a5c/features/data_transformed.tsv
2025-09-01 21:58:20.112899 INFO::Applying z-score to standardize continuous metadata
2025-09-01 21:58:20.118492 INFO::Running the linear model component
2025-09-01 21:58:20.14117 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:20.1466 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:20.152103 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:20.160197 INFO::Counting total values for each feature
2025-09-01 21:58:20.162231 INFO::Running the logistic model component
2025-09-01 21:58:20.184158 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:20.191613 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:20.199108 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:20.211493 INFO::Counting total values for each feature
2025-09-01 21:58:20.214937 INFO::Re-running abundances for warn_prevalence
2025-09-01 21:58:20.21676 INFO::Running selected normalization method: TSS
2025-09-01 21:58:20.218747 INFO::Running selected transform method: LOG
2025-09-01 21:58:20.241044 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:20.246516 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:20.25333 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:20.381236 INFO::Creating fits folder
2025-09-01 21:58:20.382861 INFO::Writing residuals to file /tmp/RtmppHDurU/file84112e344a5c/fits/residuals_linear.rds
2025-09-01 21:58:20.384506 INFO::Writing fitted values to file /tmp/RtmppHDurU/file84112e344a5c/fits/fitted_linear.rds
2025-09-01 21:58:20.386168 INFO::Writing residuals to file /tmp/RtmppHDurU/file84112e344a5c/fits/residuals_logistic.rds
2025-09-01 21:58:20.387594 INFO::Writing fitted values to file /tmp/RtmppHDurU/file84112e344a5c/fits/fitted_logistic.rds
2025-09-01 21:58:20.390479 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmppHDurU/file84112e344a5c/all_results.tsv
2025-09-01 21:58:20.392794 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/RtmppHDurU/file84112e344a5c/significant_results.tsv
2025-09-01 21:58:20.394487 INFO::Creating output figures folder
2025-09-01 21:58:20.395988 INFO::Writing summary plot of significant
results to file: /tmp/RtmppHDurU/file84112e344a5c/figures/summary_plot.pdf
2025-09-01 21:58:21.796061 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmppHDurU/file84112e344a5c/figures
2025-09-01 21:58:21.798409 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-01 21:58:21.806282 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-01 21:58:22.241559 INFO::Writing summary plot of
significant results to file: /tmp/RtmppHDurU/file84112e344a5c/figures/summary_plot.pdf
2025-09-01 21:58:23.57966 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmppHDurU/file84112e344a5c/figures
2025-09-01 21:58:23.581752 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-01 21:58:23.587622 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-01 21:58:24.029285 INFO::Running the linear model component
2025-09-01 21:58:24.03766 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:24.042606 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:24.047641 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:24.057167 INFO::Counting total values for each feature
2025-09-01 21:58:24.059357 INFO::Running the logistic model component
2025-09-01 21:58:24.071881 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:24.081685 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:24.091044 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:24.101043 INFO::Counting total values for each feature
2025-09-01 21:58:24.103062 INFO::Re-running abundances for warn_prevalence
2025-09-01 21:58:24.103974 INFO::Running selected normalization method: TSS
2025-09-01 21:58:24.105355 INFO::Running selected transform method: LOG
2025-09-01 21:58:24.114929 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:24.119575 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:24.123528 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:24.226581 INFO::Creating output folder
2025-09-01 21:58:24.228145 INFO::Creating output figures folder
2025-09-01 21:58:24.230278 INFO::Writing summary plot of significant
results to file: /tmp/RtmppHDurU/file841116f65ce8/figures/summary_plot.pdf
2025-09-01 21:58:25.668687 INFO::Writing association plots (one for each significant association) to output folder: /tmp/RtmppHDurU/file841116f65ce8/figures
2025-09-01 21:58:25.670177 INFO::Plotting associations from most to least significant, grouped by metadata
2025-09-01 21:58:25.675585 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-09-01 21:58:26.797817 INFO::Applying z-score to standardize continuous metadata
2025-09-01 21:58:26.807834 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-09-01 21:58:26.809145 INFO::Bypass z-score application to metadata
2025-09-01 21:58:26.813013 INFO::Bypass z-score application to metadata
2025-09-01 21:58:26.840708 INFO::Determining format of input files
2025-09-01 21:58:26.842166 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-01 21:58:26.843466 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-09-01 21:58:26.852634 INFO::Determining format of input files
2025-09-01 21:58:26.854011 INFO::Input format is data samples as columns and metadata samples as rows
2025-09-01 21:58:26.855394 INFO::Input format is feature_specific_covariate samples as columns
2025-09-01 21:58:26.863562 INFO::Determining format of input files
2025-09-01 21:58:26.865121 INFO::Input format is data samples as rows and metadata samples as rows
2025-09-01 21:58:26.866764 INFO::Input format is feature_specific_covariate samples as columns
2025-09-01 21:58:26.869278 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-09-01 21:58:26.87041 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-09-01 21:58:26.885041 INFO::Running selected transform method: LOG
2025-09-01 21:58:26.886928 INFO::Creating output feature tables folder
2025-09-01 21:58:26.888503 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmppHDurU/file841178725990/features/data_transformed.tsv
2025-09-01 21:58:26.893803 INFO::Running selected transform method: LOG
2025-09-01 21:58:26.895614 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmppHDurU/file841178725990/features/data_transformed.tsv
2025-09-01 21:58:26.900572 INFO::Running selected transform method: PLOG
2025-09-01 21:58:26.903181 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmppHDurU/file841178725990/features/data_transformed.tsv
2025-09-01 21:58:26.907267 INFO::Running selected transform method: NONE
2025-09-01 21:58:26.908631 INFO::Writing normalized, filtered, transformed data to file /tmp/RtmppHDurU/file841178725990/features/data_transformed.tsv
2025-09-01 21:58:26.920246 INFO::Running the linear model component
2025-09-01 21:58:26.932259 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:26.93638 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:26.941047 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:26.95 INFO::Counting total values for each feature
2025-09-01 21:58:26.95212 INFO::Running the logistic model component
2025-09-01 21:58:26.961836 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:26.968826 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:26.975699 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:26.987684 INFO::Counting total values for each feature
2025-09-01 21:58:26.99202 INFO::Re-running abundances for warn_prevalence
2025-09-01 21:58:26.993382 INFO::Running selected normalization method: TSS
2025-09-01 21:58:26.995344 INFO::Running selected transform method: LOG
2025-09-01 21:58:27.007295 INFO::Fitting model to feature number 1, a
2025-09-01 21:58:27.011782 INFO::Fitting model to feature number 2, b
2025-09-01 21:58:27.017691 INFO::Fitting model to feature number 3, c
2025-09-01 21:58:27.13055 INFO::Creating output folder
2025-09-01 21:58:27.131592 INFO::Creating fits folder
2025-09-01 21:58:27.132472 INFO::Writing residuals to file /tmp/RtmppHDurU/file84111b563ab7/fits/residuals_linear.rds
2025-09-01 21:58:27.133574 INFO::Writing fitted values to file /tmp/RtmppHDurU/file84111b563ab7/fits/fitted_linear.rds
2025-09-01 21:58:27.134771 INFO::Writing residuals to file /tmp/RtmppHDurU/file84111b563ab7/fits/residuals_logistic.rds
2025-09-01 21:58:27.136219 INFO::Writing fitted values to file /tmp/RtmppHDurU/file84111b563ab7/fits/fitted_logistic.rds
2025-09-01 21:58:27.139451 INFO::Writing all the results to file (ordered
by increasing individual q-values): /tmp/RtmppHDurU/file84111b563ab7/all_results.tsv
2025-09-01 21:58:27.14206 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/RtmppHDurU/file84111b563ab7/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
347.724 7.571 357.532
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 23.791 | 1.052 | 25.084 | |
| maaslin_check_arguments | 0.169 | 0.004 | 0.173 | |
| maaslin_check_formula | 0.173 | 0.009 | 0.185 | |
| maaslin_compute_formula | 0.151 | 0.009 | 0.163 | |
| maaslin_contrast_test | 19.390 | 0.965 | 20.512 | |
| maaslin_filter | 1.369 | 0.236 | 1.617 | |
| maaslin_fit | 13.896 | 0.763 | 14.754 | |
| maaslin_log_arguments | 0.178 | 0.009 | 0.190 | |
| maaslin_normalize | 0.385 | 0.029 | 0.419 | |
| maaslin_plot_results | 41.388 | 0.994 | 42.673 | |
| maaslin_plot_results_from_output | 42.080 | 1.126 | 43.523 | |
| maaslin_process_metadata | 0.585 | 0.039 | 0.671 | |
| maaslin_read_data | 0.157 | 0.009 | 0.166 | |
| maaslin_reorder_data | 0.175 | 0.010 | 0.187 | |
| maaslin_transform | 0.790 | 0.054 | 0.852 | |
| maaslin_write_results | 15.256 | 0.860 | 16.218 | |
| maaslin_write_results_lefse_format | 16.697 | 0.737 | 17.544 | |
| preprocess_dna_mtx | 0.005 | 0.000 | 0.005 | |
| preprocess_taxa_mtx | 0.005 | 0.001 | 0.006 | |