William Nickols
| Snapshot Date: 2025-12-10 13:40 -0500 (Wed, 10 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/maaslin3 |
| git_branch: devel |
| git_last_commit: b274055 |
| git_last_commit_date: 2025-10-29 11:33:46 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-11 11:35 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4872 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4580 |
| 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 1157/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maaslin3 1.3.0 (landing page) William Nickols
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2025-12-10 20:56:37 -0500 (Wed, 10 Dec 2025) |
| EndedAt: 2025-12-10 21:01:58 -0500 (Wed, 10 Dec 2025) |
| EllapsedTime: 321.2 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/maaslin3.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maaslin3/DESCRIPTION’ ... OK
* this is package ‘maaslin3’ version ‘1.3.0’
* 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 17.543 0.607 19.164
maaslin_plot_results 16.729 0.559 18.297
maaslin3 8.270 0.530 9.096
maaslin_contrast_test 8.029 0.709 9.224
maaslin_write_results 5.606 0.503 6.438
maaslin_fit 5.389 0.612 6.406
maaslin_write_results_lefse_format 5.560 0.416 6.290
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘maaslin3’ ... ** this is package ‘maaslin3’ version ‘1.3.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(maaslin3)
>
> test_check("maaslin3")
2025-12-10 20:59:22.582368 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 20:59:22.612097 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 20:59:22.643563 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 20:59:22.658132 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 20:59:22.681282 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 20:59:22.709311 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 20:59:22.71154 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 20:59:22.717474 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 20:59:22.763292 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 20:59:22.765451 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 20:59:22.786274 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 20:59:22.800771 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 20:59:22.80545 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 20:59:22.820489 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 20:59:22.852096 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 20:59:30.075653 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 20:59:30.106224 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 20:59:30.13322 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 20:59:30.141056 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 20:59:30.153234 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 20:59:30.192173 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 20:59:30.194177 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 20:59:30.198413 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 20:59:30.233766 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 20:59:30.235864 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 20:59:30.255825 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 20:59:30.272862 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 20:59:30.278222 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 20:59:30.292488 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 20:59:30.318878 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 20:59:31.947 R[61858:354998197] XType: Using static font registry.
2025-12-10 20:59:40.557008 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 20:59:40.586713 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 20:59:40.618818 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 20:59:40.62716 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 20:59:40.640008 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 20:59:40.668036 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 20:59:40.670476 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 20:59:40.675166 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 20:59:40.713753 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 20:59:40.715899 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 20:59:40.733492 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 20:59:40.747674 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 20:59:40.752607 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 20:59:40.769506 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 20:59:40.796539 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 20:59:46.421632 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 20:59:46.449528 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 20:59:46.4755 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 20:59:46.487438 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 20:59:46.502342 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 20:59:46.531729 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 20:59:46.533955 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 20:59:46.538384 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 20:59:46.572432 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 20:59:46.5745 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 20:59:46.594394 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 20:59:46.610747 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 20:59:46.615579 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 20:59:46.629863 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 20:59:46.655265 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 20:59:46.743874 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/residuals_linear.rds
2025-12-10 20:59:46.777838 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/fitted_linear.rds
2025-12-10 20:59:46.817965 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/residuals_logistic.rds
2025-12-10 20:59:47.012012 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/fitted_logistic.rds
2025-12-10 20:59:57.050283 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 20:59:57.076463 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 20:59:57.105235 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 20:59:57.113286 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 20:59:57.128868 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 20:59:57.157656 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 20:59:57.159778 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 20:59:57.16403 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 20:59:57.197438 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 20:59:57.199581 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 20:59:57.216614 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 20:59:57.234515 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 20:59:57.238882 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 20:59:57.258483 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 20:59:57.282671 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:00:02.351383 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:00:02.377529 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:00:02.404809 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:00:02.41479 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:00:02.428576 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:00:02.4551 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:00:02.456984 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:00:02.461014 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:00:02.496035 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:00:02.502211 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:00:02.522059 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:00:02.535998 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:00:02.5403 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:00:02.55454 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:00:02.584501 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:00:02.689069 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/residuals_linear.rds
2025-12-10 21:00:02.7249 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/fitted_linear.rds
2025-12-10 21:00:02.766729 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/residuals_logistic.rds
2025-12-10 21:00:02.950878 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/fitted_logistic.rds
2025-12-10 21:00:11.843775 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:00:11.875591 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:00:11.903985 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:00:11.912401 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:00:11.924827 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:00:11.952029 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:00:11.954175 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:00:11.958523 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:00:11.994776 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:00:11.997249 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:00:12.017486 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:00:12.031821 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:00:12.042288 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:00:12.059821 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:00:12.085448 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:00:17.301787 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:00:17.330762 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:00:17.362853 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:00:17.37035 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:00:17.381958 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:00:17.409253 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:00:17.411225 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:00:17.415359 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:00:17.453378 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:00:17.455615 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:00:17.476575 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:00:17.490567 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:00:17.495455 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:00:17.511433 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:00:17.540048 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:00:17.629392 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/residuals_linear.rds
2025-12-10 21:00:17.663949 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/fitted_linear.rds
2025-12-10 21:00:17.701378 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/residuals_logistic.rds
2025-12-10 21:00:17.889613 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2590c2612/fits/fitted_logistic.rds
2025-12-10 21:00:26.71404 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:00:26.748997 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:00:26.77702 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:00:26.785431 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:00:26.800142 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:00:26.829513 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:00:26.831839 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:00:26.836494 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:00:26.878642 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:00:26.880932 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:00:26.900336 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:00:26.91465 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:00:26.91897 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:00:26.937625 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:00:26.961957 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:00:32.831147 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:00:32.860769 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:00:32.889319 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:00:32.89708 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:00:32.909554 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:00:32.936567 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:00:32.938633 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:00:32.942738 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:00:32.980023 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:00:32.98235 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:00:32.999197 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:00:33.012992 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:00:33.017549 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:00:33.031912 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:00:33.058908 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:00:43.017643 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:00:47.086348 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:00:57.530228 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:01:01.613391 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:01:01.841915 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_linear.rds
2025-12-10 21:01:01.876413 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_linear.rds
2025-12-10 21:01:01.898828 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_logistic.rds
2025-12-10 21:01:01.944049 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_logistic.rds
2025-12-10 21:01:11.620773 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:01:14.373797 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:01:14.50441 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_linear.rds
2025-12-10 21:01:14.537816 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_linear.rds
2025-12-10 21:01:14.565293 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_logistic.rds
2025-12-10 21:01:14.610043 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_logistic.rds
2025-12-10 21:01:22.717771 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:01:25.582249 WARNING::Fitting problem for feature 124 returning NA
2025-12-10 21:01:25.688761 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_linear.rds
2025-12-10 21:01:25.722315 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_linear.rds
2025-12-10 21:01:25.748048 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_logistic.rds
2025-12-10 21:01:25.796275 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_logistic.rds
2025-12-10 21:01:33.547753 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:01:33.577914 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:01:33.614165 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:01:33.622267 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:01:33.634813 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:01:33.667289 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:01:33.669694 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:01:33.67416 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:01:33.707813 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:01:33.709972 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:01:33.729568 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:01:33.744673 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:01:33.749436 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:01:33.764794 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:01:33.813413 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:01:39.109495 WARNING::Fitting problem for feature 50 returning NA
2025-12-10 21:01:39.135747 WARNING::Fitting problem for feature 62 returning NA
2025-12-10 21:01:39.163507 WARNING::Fitting problem for feature 74 returning NA
2025-12-10 21:01:39.171319 WARNING::Fitting problem for feature 78 returning NA
2025-12-10 21:01:39.183296 WARNING::Fitting problem for feature 84 returning NA
2025-12-10 21:01:39.210237 WARNING::Fitting problem for feature 96 returning NA
2025-12-10 21:01:39.212363 WARNING::Fitting problem for feature 97 returning NA
2025-12-10 21:01:39.216599 WARNING::Fitting problem for feature 99 returning NA
2025-12-10 21:01:39.25266 WARNING::Fitting problem for feature 114 returning NA
2025-12-10 21:01:39.255204 WARNING::Fitting problem for feature 115 returning NA
2025-12-10 21:01:39.274609 WARNING::Fitting problem for feature 123 returning NA
2025-12-10 21:01:39.289489 WARNING::Fitting problem for feature 130 returning NA
2025-12-10 21:01:39.293917 WARNING::Fitting problem for feature 132 returning NA
2025-12-10 21:01:39.30871 WARNING::Fitting problem for feature 139 returning NA
2025-12-10 21:01:39.337481 WARNING::Fitting problem for feature 150 returning NA
2025-12-10 21:01:39.466361 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_linear.rds
2025-12-10 21:01:39.501476 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_linear.rds
2025-12-10 21:01:39.536598 WARNING::Deleting existing residuals file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/residuals_logistic.rds
2025-12-10 21:01:39.720177 WARNING::Deleting existing fitted file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a2de88ad2/fits/fitted_logistic.rds
2025-12-10 21:01:48.226807 ERROR::Please select a normalization from the list of available options : TSS, CLR, NONE
2025-12-10 21:01:48.232539 ERROR::Please select a transform from the list of available options : LOG, PLOG, NONE
2025-12-10 21:01:48.236389 ERROR::Please select a correction method from the list of available options : BH, holm, hochberg, hommel, bonferroni, BY
2025-12-10 21:01:48.255474 ERROR::No fixed, group, or
ordered effects included in formula.
2025-12-10 21:01:48.261211 ERROR::Effect name not found in metadata: d
2025-12-10 21:01:48.264977 ERROR::No user formula provided
2025-12-10 21:01:48.275117 ERROR::Effect name not found in metadata so not applied to formula as random effect: d
2025-12-10 21:01:48.279178 ERROR::No fixed/group/ordered/
feature-specific effects provided.
2025-12-10 21:01:49.563096 INFO::Writing function arguments to log file
2025-12-10 21:01:49.569447 INFO::Verifying options selected are valid
2025-12-10 21:01:50.535278 INFO::Writing function arguments to log file
2025-12-10 21:01:50.539656 INFO::Verifying options selected are valid
2025-12-10 21:01:50.540008 INFO::Determining format of input files
2025-12-10 21:01:50.540303 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-10 21:01:50.54106 INFO::Running selected normalization method: TSS
2025-12-10 21:01:50.541565 INFO::Creating output feature tables folder
2025-12-10 21:01:50.541933 INFO::Writing normalized data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/features/data_norm.tsv
2025-12-10 21:01:50.542476 INFO::Filter data based on min abundance, min prevalence, and max prevalence
2025-12-10 21:01:50.542764 INFO::Total samples in data: 16
2025-12-10 21:01:50.543033 INFO::Min samples required with min abundance for a feature not to be filtered: 0.000000
2025-12-10 21:01:50.543297 INFO::Max samples allowed with min abundance for a feature not to be filtered: 16.160000
2025-12-10 21:01:50.543903 INFO::Total filtered features: 0
2025-12-10 21:01:50.544229 INFO::Filtered feature names from abundance, min prevalence, and max prevalence filtering:
2025-12-10 21:01:50.544596 INFO::Total features filtered by non-zero variance filtering: 0
2025-12-10 21:01:50.544891 INFO::Filtered feature names from variance filtering:
2025-12-10 21:01:50.545177 INFO::Writing filtered data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/features/filtered_data.tsv
2025-12-10 21:01:50.545684 INFO::Running selected transform method: LOG
2025-12-10 21:01:50.54606 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/features/data_transformed.tsv
2025-12-10 21:01:50.546629 INFO::Applying z-score to standardize continuous metadata
2025-12-10 21:01:50.548773 INFO::Running the linear model component
2025-12-10 21:01:50.555229 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:50.557399 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:50.561776 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:50.567778 INFO::Counting total values for each feature
2025-12-10 21:01:50.568687 INFO::Running the logistic model component
2025-12-10 21:01:50.57425 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:50.576528 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:50.578442 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:50.581722 INFO::Counting total values for each feature
2025-12-10 21:01:50.582566 INFO::Re-running abundances for warn_prevalence
2025-12-10 21:01:50.58301 INFO::Running selected normalization method: TSS
2025-12-10 21:01:50.583579 INFO::Running selected transform method: LOG
2025-12-10 21:01:50.589005 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:50.59042 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:50.591701 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:50.625723 INFO::Creating fits folder
2025-12-10 21:01:50.633585 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/fits/residuals_linear.rds
2025-12-10 21:01:50.634294 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/fits/fitted_linear.rds
2025-12-10 21:01:50.634817 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/fits/residuals_logistic.rds
2025-12-10 21:01:50.635351 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/fits/fitted_logistic.rds
2025-12-10 21:01:50.636484 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/all_results.tsv
2025-12-10 21:01:50.637283 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/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/significant_results.tsv
2025-12-10 21:01:50.637878 INFO::Creating output figures folder
2025-12-10 21:01:50.638454 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/figures/summary_plot.pdf
2025-12-10 21:01:51.323439 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/figures
2025-12-10 21:01:51.324368 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-10 21:01:51.326605 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-10 21:01:51.541869 INFO::Writing summary plot of
significant results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/figures/summary_plot.pdf
2025-12-10 21:01:52.222011 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a230218cd5/figures
2025-12-10 21:01:52.222658 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-10 21:01:52.224688 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-10 21:01:52.464714 INFO::Running the linear model component
2025-12-10 21:01:52.468457 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:52.470385 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:52.471992 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:52.475 INFO::Counting total values for each feature
2025-12-10 21:01:52.475652 INFO::Running the logistic model component
2025-12-10 21:01:52.478736 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:52.488266 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:52.490454 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:52.493913 INFO::Counting total values for each feature
2025-12-10 21:01:52.494763 INFO::Re-running abundances for warn_prevalence
2025-12-10 21:01:52.495038 INFO::Running selected normalization method: TSS
2025-12-10 21:01:52.495555 INFO::Running selected transform method: LOG
2025-12-10 21:01:52.498402 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:52.499853 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:52.501061 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:52.532342 INFO::Creating output folder
2025-12-10 21:01:52.532838 INFO::Creating output figures folder
2025-12-10 21:01:52.533308 INFO::Writing summary plot of significant
results to file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a27b0b723/figures/summary_plot.pdf
2025-12-10 21:01:53.204006 INFO::Writing association plots (one for each significant association) to output folder: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a27b0b723/figures
2025-12-10 21:01:53.204604 INFO::Plotting associations from most to least significant, grouped by metadata
2025-12-10 21:01:53.20649 INFO::Creating boxplot for continuous data (logistic), var1 vs a
2025-12-10 21:01:53.650938 INFO::Applying z-score to standardize continuous metadata
2025-12-10 21:01:53.653704 INFO::Factor detected for categorial metadata 'c'. Using as-is.
2025-12-10 21:01:53.653988 INFO::Bypass z-score application to metadata
2025-12-10 21:01:53.654767 INFO::Bypass z-score application to metadata
2025-12-10 21:01:53.661945 INFO::Determining format of input files
2025-12-10 21:01:53.662255 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-10 21:01:53.662508 INFO::Input format is data samples as rows and feature_specific_covariate samples as rows
2025-12-10 21:01:53.664973 INFO::Determining format of input files
2025-12-10 21:01:53.665306 INFO::Input format is data samples as columns and metadata samples as rows
2025-12-10 21:01:53.665698 INFO::Input format is feature_specific_covariate samples as columns
2025-12-10 21:01:53.668271 INFO::Determining format of input files
2025-12-10 21:01:53.668567 INFO::Input format is data samples as rows and metadata samples as rows
2025-12-10 21:01:53.668869 INFO::Input format is feature_specific_covariate samples as columns
2025-12-10 21:01:53.66933 INFO::The following samples were found to have metadata but no features (or feature specific covariates if applicable). They will be removed. sample1
2025-12-10 21:01:53.669548 INFO::The following samples were found to have feature specific covariates but no features or no metadata. They will be removed. sample1
2025-12-10 21:01:53.673469 INFO::Running selected transform method: LOG
2025-12-10 21:01:53.673815 INFO::Creating output feature tables folder
2025-12-10 21:01:53.674184 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a24fab530d/features/data_transformed.tsv
2025-12-10 21:01:53.675514 INFO::Running selected transform method: LOG
2025-12-10 21:01:53.675832 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a24fab530d/features/data_transformed.tsv
2025-12-10 21:01:53.677029 INFO::Running selected transform method: PLOG
2025-12-10 21:01:53.677519 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a24fab530d/features/data_transformed.tsv
2025-12-10 21:01:53.678449 INFO::Running selected transform method: NONE
2025-12-10 21:01:53.67869 INFO::Writing normalized, filtered, transformed data to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a24fab530d/features/data_transformed.tsv
2025-12-10 21:01:53.681434 INFO::Running the linear model component
2025-12-10 21:01:53.684139 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:53.68553 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:53.686715 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:53.688991 INFO::Counting total values for each feature
2025-12-10 21:01:53.689528 INFO::Running the logistic model component
2025-12-10 21:01:53.692038 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:53.693941 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:53.695696 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:53.698524 INFO::Counting total values for each feature
2025-12-10 21:01:53.69923 INFO::Re-running abundances for warn_prevalence
2025-12-10 21:01:53.699474 INFO::Running selected normalization method: TSS
2025-12-10 21:01:53.699904 INFO::Running selected transform method: LOG
2025-12-10 21:01:53.702629 INFO::Fitting model to feature number 1, a
2025-12-10 21:01:53.704076 INFO::Fitting model to feature number 2, b
2025-12-10 21:01:53.705311 INFO::Fitting model to feature number 3, c
2025-12-10 21:01:53.732677 INFO::Creating output folder
2025-12-10 21:01:53.733137 INFO::Creating fits folder
2025-12-10 21:01:53.736689 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a278d9a357/fits/residuals_linear.rds
2025-12-10 21:01:53.737256 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a278d9a357/fits/fitted_linear.rds
2025-12-10 21:01:53.737693 INFO::Writing residuals to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a278d9a357/fits/residuals_logistic.rds
2025-12-10 21:01:53.738115 INFO::Writing fitted values to file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a278d9a357/fits/fitted_logistic.rds
2025-12-10 21:01:53.739146 INFO::Writing all the results to file (ordered
by increasing individual q-values): /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a278d9a357/all_results.tsv
2025-12-10 21:01:53.739794 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/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpoxmyYX/filef1a278d9a357/significant_results.tsv
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 95 ]
>
>
> proc.time()
user system elapsed
144.754 4.505 156.414
maaslin3.Rcheck/maaslin3-Ex.timings
| name | user | system | elapsed | |
| maaslin3 | 8.270 | 0.530 | 9.096 | |
| maaslin_check_arguments | 0.061 | 0.001 | 0.065 | |
| maaslin_check_formula | 0.058 | 0.005 | 0.064 | |
| maaslin_compute_formula | 0.078 | 0.005 | 0.084 | |
| maaslin_contrast_test | 8.029 | 0.709 | 9.224 | |
| maaslin_filter | 0.232 | 0.020 | 0.276 | |
| maaslin_fit | 5.389 | 0.612 | 6.406 | |
| maaslin_log_arguments | 0.064 | 0.003 | 0.071 | |
| maaslin_normalize | 0.142 | 0.013 | 0.163 | |
| maaslin_plot_results | 16.729 | 0.559 | 18.297 | |
| maaslin_plot_results_from_output | 17.543 | 0.607 | 19.164 | |
| maaslin_process_metadata | 0.232 | 0.022 | 0.276 | |
| maaslin_read_data | 0.055 | 0.004 | 0.066 | |
| maaslin_reorder_data | 0.055 | 0.005 | 0.064 | |
| maaslin_transform | 0.301 | 0.035 | 0.347 | |
| maaslin_write_results | 5.606 | 0.503 | 6.438 | |
| maaslin_write_results_lefse_format | 5.560 | 0.416 | 6.290 | |
| preprocess_dna_mtx | 0.001 | 0.000 | 0.004 | |
| preprocess_taxa_mtx | 0.002 | 0.000 | 0.001 | |